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Cloning and characterization of a gene encoding MIZ1, a domain of unknown function protein and its role in salt and drought stress in rice

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Abstract

Dwindling fresh water resources and climate change poses serious threats to rice production. Roots play crucial role in sensing water gradient and directing growth of the plant towards water through a mechanism called hydrotropism. Since very little information is available on root hydrotropism in major food crops, this study was carried out to clone and characterize an ortholog of Arabidopsis MIZU-KUSSEI1 (MIZ1) from rice. Contrasting rice genotypes for drought and salt tolerance were selected based on phenotyping for root traits. Nagina 22 and CR-262-4 were identified as most tolerant and Pusa Sugandh 5 and Pusa Basmati 1121 were identified as most susceptible varieties for both drought and salt stresses. Allele mining of MIZ1 in these varieties identified a 12 bp Indel but did not show specific allelic association with stress tolerance. Analysis of allelic variation of OsMIZ1 in 3024 rice genotypes of 3K genome lines using Rice SNP-Seek database revealed 49 InDels. Alleles with the 12 bp deletions were significantly prevalent in indica group as compared to that of japonica group. Real-time RT-PCR analysis revealed that OsMIZ1 expression levels were upregulated significantly in tolerant cv. Nagina 22 and CR-262-4 under osmotic stress, while under salt stress, it was significantly upregulated only in CR-262-4 but maintained in Nagina 22 under salt stress. However, in the roots of susceptible genotypes, OsMIZ1 expression decreased under both the stresses. These results highlight the possible involvement of OsMIZ1 in drought and salt stress tolerance in rice. Furthermore, expression studies using publically available resources showed that enhanced expression of OsMIZ1 is regulated in response to disease infections, mineral deficiency, and heavy metal stresses and is also expressed in reproductive tissues in addition to roots. These findings indicate potential involvement of MIZ1 in developmental and stress response processes in rice.

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Acknowledgments

Authors acknowledge the support of Director, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, for carrying out this work.

Funding

National Agriculture Science Fund (NASF), ICAR, New Delhi, Grant No. Phen 2015/2011-12 financially supported phenotyping and cloning and expression analysis.

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Authors and Affiliations

  1. ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India

    Vikender Kaur, Dhammaprakash P. Wankhede, Pranusha Pulivendula & Ashok Kumar

  2. Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India

    Shashank K. Yadav & Viswanathan Chinnusamy

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  1. Vikender Kaur
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  2. Shashank K. Yadav
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  3. Dhammaprakash P. Wankhede
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  4. Pranusha Pulivendula
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  6. Viswanathan Chinnusamy
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Contributions

Conceived and designed the experiments-VK, PP, VC; performed the experiments-VK, SKY, PP; bioinformatics work and data analysis-DPW, VK; manuscript drafting-VK, DPW, AK, VC.

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Correspondence to Vikender Kaur or Viswanathan Chinnusamy.

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Supplementary Table S1

(DOCX 14 kb)

Supplementary Fig. S1

Root phenotypes of drought tolerant and susceptible varieties in response to drought stress (PEG 15%) (JPG 255 kb)

Supplementary Fig. S2

Gene structure of rice MIZ1. Coding sequence and genomic sequence of MIZ1 was used to develop graphics for visualization using Gene structure display server program. Filled boxes in maroon color indicate 5‘ and 3‘ UTR, filled boxes in green indicate exons and lines joining two exons indicate intron (JPG 17 kb)

Supplementary Fig. S3

Allele count of locus Loc_Os02g47980 (OsMIZ1) in 3024 accessions from SNP-seek database. Allele count in different rice subpopulations have been indicated by distinct lines. On X-axis numbers represent positions of Indels. Number on Y-axis indicates allele numbers (JPG 80 kb)

Supplementary Fig. S4

Expression of OsMIZ1 (Loc_Os02g47980) in rice genotypes FL478 and IR29 in response to salt stress. The expression data is retrieved from Genevestigator micro array data in Experiment ID, OS-00023. The scale represent percentage of expression potential with the maximum value is displayed as dark colored and minimum value is displayed as no color (JPG 34 kb)

Supplementary Fig. S5

Expression of OsMIZ1 (Loc_Os02g47980) in rice varieties IRAT109 and ZS97 for drought stress treatment in flag leaves. The expression data is retrieved from Genevestigator micro array data in Experiment ID, OS-00068. The scale represent percentage of expression potential with the maximum value is displayed as dark colored and minimum value is displayed as no color (JPG 69 kb)

Supplementary Fig. S6

Expression of OsMIZ1 (Loc_Os02g47980) during reproductive development in rice variety IR64. The expression data is retrieved from Genevestigator micro array data in Experiment ID, OS-00007. The scale represent percentage of expression potential with the maximum value is displayed as dark colored and minimum value is displayed as no color (JPG 112 kb)

Supplementary Fig. S7

Expression of OsMIZ1 (Loc_Os02g47980) in response to different strains/mutants of Xanthomonas oryzae in two susceptible rice cultivars, nipponbare and IR24. PXO99A, T7174, and PXO86 are wild type strains of Xanthomonas oryzae pv. oryzae (Xoo). PXO99AME1 is double mutant of effectors, a pthXo6 and avrXa27. PXO99AME2 is mutant of an effector, pthXo1. PXO99ME5 is a reduced virulence strain with uncharacterized mutation in a TAL effector; and strain PXO99AME7 has nonfunctional type III secretion system, non-pathogenic. The expression data is retrieved from Genevestigator micro array data in Experiment ID, OS-00061. The scale represent percentage of expression potential with the maximum value is displayed as dark colored and minimum value is displayed as no color (JPG 276 kb)

Supplementary Fig. S8

OsMIZ1 (Loc_Os02g47980) expression in roots of rice variety IR64 upon treatment with different heavy metals. The expression data is retrieved from Genevestigator micro array data in Experiment ID, OS-00040. The scale represent percentage of expression potential with the maximum value is displayed as dark colored and minimum value is displayed as no color (JPG 58 kb)

Supplementary Fig. S9

OsMIZ1 (Loc_Os02g47980) expression in rice cultivar Zhonghua11 in response to heat (42°C) treatment. The expression data is retrieved from Genevestigator micro array data in Experiment ID, OS-00024. The scale represent percentage of expression potential with the maximum value is displayed as dark colored and minimum value is displayed as no color (JPG 27 kb)

Supplementary Fig. S10

Co-expression of genes with OsMIZ1 (Loc_Os02g47980) in response nutrient media deficient in either Phosphorus (P) / Iron (Fe) or both. Lines of different colors shows co-expression patterns of genes. OsMIZ1 expression is indicated with line in red color. The locus ID of co-expressing genes along with functional annotation and their respective line color in plot on left side is mentioned in table on the right side. X axis shows different combination of nutrient media with/without Fe/P. Y axis indicates expression values in terms of Z-score. Cut off value for gene co-expression was between 0.95 and 1. Gene co-expression plot was drawn using experiment ‘Iron and phosphorus interaction in rice seedlings’ in module GSE17245-turquoise at Rice Genome annotation project database (JPG 123 kb)

Supplementary Fig. S11

Co-expression analysis of OsMIZ1 (Loc_Os02g47980) (JPG 226 kb)

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Kaur, V., Yadav, S.K., Wankhede, D.P. et al. Cloning and characterization of a gene encoding MIZ1, a domain of unknown function protein and its role in salt and drought stress in rice. Protoplasma 257, 475–487 (2020). https://doi.org/10.1007/s00709-019-01452-5

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