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Construction and analysis of an Oryza sativa (cv. MR219) salinity-related cDNA library

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Abstract

To identify salt-responsive genes, we constructed a cDNA subtractive library from a salt-tolerant rice cultivar, MR219. Treatments of the whole plant were carried out with 150 mM sodium chloride for 0, 2, 4, 8, 12 and 24 h. The extraction of total RNA from 14-day-old seedlings was conducted on the shoots and roots of both treated and untreated plants. The treated plants were utilized as ‘drivers’ while the untreated plants were utilized as ‘testers’. Equal amounts of the extracted total RNA from the 12 samples were pooled together and subjected to mRNA isolation. A reverse transcription of tester and driver cDNAs from the mRNA of two pools of the samples was conducted. In total, 300 clones were sequenced and analysed using bioinformatics tools. The 260 high-quality sequences were assembled and 83 contigs and 42 singletons were generated, producing a total of 125 UTs. The majority of the UTs showed significant homology with sequences in the NCBI database. A total of 330 gene ontology terms were grouped into three categories, of which 144 UTs fell under biological process, 108 fell under cellular component and 78 fell under molecular function. Also, RT-PCR was utilized to substantiate the elevation in expression of six candidate genes ((MR219SAP8 (JZ532324) and salT (JZ532363), low molecular weight heat shock (JZ532334), phospholipid hydroperoxide glutathione (JZ532371), Acetamidase (JZ532408), Ferredoxin-1 and chloroplastic (JZ532374)) subjected to salinity stress at varying timepoints.

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Abbreviations

cDNA:

DNA complementary to RNA

MR219:

MARDI rice 219

UTs:

Unique transcripts

NCBI:

National centre for biotechnology information

RT-PCR:

Reverse transcription polymerase chain reaction

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Acknowledgments

This research is founded by grants PJ008574 from National Academy of Agricultural Science, RDA, Suwon, Korea and ERSTS/1/2012/STG08/UKM/02/11, Malaysia awarded to Prof. Zamri Zainal.

Conflict of interest

The authors declare that there is no conflict of interest regarding the publication of this paper.

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Authors and Affiliations

  1. School of Biosciences and Biotechnology, Faculty Science and Technology, UKM, 43600, Bangi, Selangor, Malaysia

    Poya Hedayati, Hossein Hosseni Monfard, Nurulhikma Md Isa, Che Radziah Che Mohd Zain, Md. Imtiaz Uddin, Ismanizan Ismail & Zamri Zainal

  2. Institute of Systems Biology (INBIOSIS), UKM, 43600, Bangi, Selangor, Malaysia

    Poya Hedayati, Hossein Hosseni Monfard, Md. Imtiaz Uddin & Zamri Zainal

  3. National Academy of Agricultural Science, RDA, Suwon, 441-857, Korea

    Duk Ju Hwang

  4. Biotechnology Research Centre, MARDI Headquarters, Persiaran MARDI-UPM, 43400, Serdang, Selangor, Malaysia

    Ab Rahman Zuraida

Authors
  1. Poya Hedayati
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  2. Hossein Hosseni Monfard
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  3. Nurulhikma Md Isa
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  5. Che Radziah Che Mohd Zain
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  8. Ismanizan Ismail
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  9. Zamri Zainal
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Corresponding author

Correspondence to Zamri Zainal.

Additional information

Communicated by S. Abe.

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Hedayati, P., Monfard, H.H., Isa, N.M. et al. Construction and analysis of an Oryza sativa (cv. MR219) salinity-related cDNA library. Acta Physiol Plant 37, 91 (2015). https://doi.org/10.1007/s11738-015-1837-4

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  • DOI: https://doi.org/10.1007/s11738-015-1837-4

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