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

Abstract

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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References

  1. Akpinar B, Canli O, Budak H (2015) Zn-deficiency responsive transcripts in Agrostis species revealed by mRNA differential display. In: Budak H, Spangenberg G (eds) Molecular breeding of forage and turf. Springer, Cham, pp 69–84

    Google Scholar 

  2. Arnold TIM, Kirk GJ, Wissuwa M, Frei M, Zhao FJ, Mason TF, Weiss DJ (2010) Evidence for the mechanisms of zinc uptake by rice using isotope fractionation. Plant Cell Environ 33:370–381

    CAS  Article  PubMed  Google Scholar 

  3. Arnon DI (1949) Copper enzymes in isolated chloroplasts: polyphenoloxidase in Beta vulgaris. Plant Physiol 24:1–15

  4. Assunção AG, Herrero E, Lin YF, Huettel B, Talukdar S, Smaczniak C, Immink RG, Van Eldik M, Fiers M, Schat H, Aarts MG (2010) Arabidopsis thaliana transcription factors bZIP19 and bZIP23 regulate the adaptation to zinc deficiency. Proc Natl Acad Sci U S A 107:10296–10301

    Article  PubMed  PubMed Central  Google Scholar 

  5. Broadley MR, White PJ, Hammond JP, Zelko I, Lux A (2007) Zinc in plants. New Phytol 173:677–702

    CAS  Article  PubMed  Google Scholar 

  6. Cakmak I (2000) Possible roles of zinc in protecting plant cells from damage by reactive oxygen species. New Phytol 146:185–205

    CAS  Article  Google Scholar 

  7. Cao PJ, Bartley LE, Jung KH, Ronald PC (2008) Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases. Mol Plant 1:858–877

    CAS  Article  PubMed  Google Scholar 

  8. Chen W, Yang X, He Z, Feng Y, Hu F (2008) Differential changes in photosynthetic capacity, 77 K chlorophyll fluorescence and chloroplast ultrastructure between Zn-efficient and Zn-inefficient rice genotypes (Oryza sativa) under low zinc stress. Physiol Plantarum 132:89–101

    CAS  Article  Google Scholar 

  9. Curie C, Cassin G, Couch D, Divol F, Higuchi K, Le Jean M, Misson J, Schikora A, Czernic P, Mari S (2009) Metal movement within the plant: contribution of nicotianamine and yellow stripe 1-like transporters. Ann Bot 103:1–11

    CAS  Article  PubMed  Google Scholar 

  10. Dao TT, Linthorst HJ, Verpoorte R (2011) Chalcone synthase and its functions in plant resistance. Phytochem Rev 10:397–412

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Distelfeld A, Cakmak I, Peleg Z, Ozturk L, Yazici AM, Budak H, Saranga Y, Fahima T (2006) Multiple QTL-effects of wheat Gpc-B1 locus on grain protein and micronutrient concentrations. Physiol Plant 129:635–643

  12. Durmaz E, Coruh C, Dinler G, Grusak MA, Peleg Z, Saranga Y, Fahima T, Yazici A, Ozturk L, Cakmak I, Budak H (2011) Expression and cellular localization of ZIP1 transporter under zinc deficiency in wild emmer wheat. Plant Mol Biol Rep 29:582–596

    CAS  Article  Google Scholar 

  13. Englbrecht CC, Schoof H, Böhm S (2004) Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 5:39

    Article  PubMed  PubMed Central  Google Scholar 

  14. Gao J, Yu X, Ma F, Li J (2014) RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic). PLoS One 9:e88804

    Article  PubMed  PubMed Central  Google Scholar 

  15. Girke T, Lauricha J, Tran H, Keegstra K, Raikhel N (2004) The cell wall navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol 136:3003–3008

  16. Hoffland E, Wei C, Matthias W (2006) Organic anion exudation by lowland rice (Oryza sativa L.) at zinc and phosphorus deficiency. Plant Soil 15:155–162

    Article  Google Scholar 

  17. Impa SM, Gramlich A, Tandy S, Schulin R, Frossard E, Johnson-Beebout SE (2013) Internal Zn allocation influences Zn deficiency tolerance and grain Zn loading in rice (Oryza sativa L.). Front Plant Sci 4:534

  18. Ishimaru Y, Bashir K, Nishizawa NK (2011) Zn uptake and translocation in rice plants. Rice 4:21–27

    Article  Google Scholar 

  19. Ismail AM, Heuer S, Thomson JT, Wissuwa M (2007) Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Mol Biol 65:547–570

    CAS  Article  PubMed  Google Scholar 

  20. Martin LBB, Fei Z, Giovannoni JJ, Rose JKC (2013) Catalyzing plant science research with RNA-seq. Front Plant Sci 4:66

    Article  PubMed  PubMed Central  Google Scholar 

  21. Ouyang SQ, Liu YF, Liu P, Lei G, He SJ, Ma B, Zhang WK, Zhang JS, Chen SY (2010) Receptor-like kinase OsSIK1 improves drought and salt stress tolerance in rice (Oryza sativa) plants. Plant J 62:316–329

    CAS  Article  PubMed  Google Scholar 

  22. Peleg Z, Cakmak I, Ozturk L, Yazici A, Jun Y, Budak H, Korol AB, Fahima T, Saranga Y (2009) Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat× wild emmer wheat RIL population. Theor Appl Genet 119:353–369

    CAS  Article  PubMed  Google Scholar 

  23. Ptashnyk M, Roose T, Jones DL, Kirk GJD (2011) Enhanced zinc uptake by rice through phytosiderophore secretion: a modelling study. Plant Cell Environ 34:2038–2046

    CAS  Article  PubMed  Google Scholar 

  24. Qadar A (2002) Selecting rice genotypes tolerant to zinc deficiency and sodicity stresses. I. Differences in zinc, iron, manganese, copper, phosphorus concentrations, and phosphorus/zinc ratio in their leaves. J Plant Nutr 25:457–473

    CAS  Article  Google Scholar 

  25. Rengel Z, Graham RD (1996) Uptake of zinc from chelate-buffered nutrient solutions by wheat genotypes differing in zinc efficiency. J Exp Bot 47:217–226

    CAS  Article  Google Scholar 

  26. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110

    CAS  Article  PubMed  Google Scholar 

  27. Sadeghzadeh B (2013) A review of zinc nutrition and plant breeding. J Soil Sci Plant Nutr 13:905–927

    Google Scholar 

  28. Sasaki H, Hirose T, Watanabe Y, Ohsugi R (1998) Carbonic anhydrase activity and CO2-transfer resistance in Zn-deficient rice leaves. Plant Physiol 118:929–934

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. Schiller M, Hegelund JN, Pedas P, Kichey T, Laursen KH, Husted S, Schjoerring JK (2014) Barley metallothioneins differ in ontogenetic pattern and response to metals. Plant Cell Environ 37:353–367

    CAS  Article  PubMed  Google Scholar 

  30. Singh AP, Pandey BK, Deveshwar P, Narnoliya L, Parida SK, Giri J (2015) JAZ repressors: potential involvement in nutrients deficiency response in rice and chickpea. Front Plant Sci 6:975

    PubMed  PubMed Central  Google Scholar 

  31. Smith KS, Ferry JG (2000) Prokaryotic carbonic anhydrases. FEMS Microbio Rev 24:335–366

    CAS  Article  Google Scholar 

  32. Suzuki M, Bashir K, Inoue H, Takahashi M, Nakanishi H, Nishizawa NK (2012) Accumulation of starch in Zn-deficient rice. Rice 5:1–8

    CAS  Article  Google Scholar 

  33. Suzuki M, Takahashi M, Tsukamoto T, Watanabe S, Matsuhashi S, Yazaki J, Kishimoto N, Kikuchi S, Nakanishi H, Mori S, Nishizawa NK (2006) Biosynthesis and secretion of mugineic acid family phytosiderophores in zinc-deficient barley. Plant J 48:85–97

    CAS  Article  PubMed  Google Scholar 

  34. Takehisa H, Sato Y, Igarashi M, Abiko T, Antonio BA, Kamatsuki K, Minami H, Namiki N, Inukai Y, Nakazono M, Nagamura Y (2012) Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions. Plant J 69:126–140

    CAS  Article  PubMed  Google Scholar 

  35. Talke IN, Hanikenne M, Krämer U (2006) Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis halleri. Plant Physiol 142:148–167

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Tennstedt P, Peisker D, Bottcher C, Trampczynska A, Clemens S (2008) Phytochelatin synthesis is essential for the detoxification of excess zinc and contributes significantly to the accumulation of zinc. Plant Physiol 149:938–948

    Article  PubMed  Google Scholar 

  37. Wang H, Jin JY (2005) Photosynthetic rate, chlorophyll fluorescence parameters, and lipid peroxidation of maize leaves as affected by zinc deficiency. Photosynthetica 12:591–596

    Article  Google Scholar 

  38. Widodo B, Broadley MR, Rose T, Frei M, Pariasca-Tanaka J, Yoshihashi T, Thomson M, Hammond JP, Aprile A, Close TJ, Ismail AM, Wissuwa M (2010) Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity. New Phytol 186:400–414

    Article  PubMed  Google Scholar 

  39. Wissuwa M, Ismail AM, Yanagihara S (2006) Effects of zinc deficiency on rice growth and genetic factors contributing to tolerance. Plant Physiol 142:731–741

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. Xu HW, Ji XM, He ZH, Shi WP, Zhu GH, Niu JK et al (2006) Oxalate accumulation and regulation is independent of glycolate oxidase in rice leaves. J Exp Bot 57:18990–11908

    Google Scholar 

  41. Ye B, Maret W, Vallee BL (2001) Zinc metallothionein imported into liver mitochondria modulates respiration. Proc Natl Acad Sci U S A 98:2317–2322

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Yoshida S, Forno DA, Cock JH, Gomez KA (1976) Laboratory manual for physiological studies of rice, 3rd edn. International Rice Research Institute, Manila, p 83

  43. Zhu JK (2001) Plant salt tolerance. Trends Plant Sci 6:66–72

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

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). https://doi.org/10.1007/s10142-017-0556-x

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Keywords

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