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

Poya Hedayati, Hossein Hosseni Monfard, Nurulhikma Md Isa, Duk Ju Hwang, Che Radziah Che Mohd. Zain, Md Imtiaz Uddin, Ab Rahman Zuraida, Ismanizan Ismail, Zamri Zainal

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
JournalActa Physiologiae Plantarum
Volume37
Issue number5
DOIs
Publication statusPublished - 1 May 2015

Fingerprint

Salinity
Gene Library
cDNA libraries
Oryza sativa
salinity
Salts
salts
RNA
Biological Phenomena
Ferredoxins
Messenger RNA
Gene Ontology
ferredoxins
reverse transcription
genes
hydroperoxides
Sequence Homology
Computational Biology
Seedlings
bioinformatics

Keywords

  • cDNA subtractive library
  • Driver
  • MR219
  • Salt-responsive genes
  • Tester

ASJC Scopus subject areas

  • Plant Science
  • Physiology
  • Agronomy and Crop Science

Cite this

Construction and analysis of an Oryza sativa (cv. MR219) salinity-related cDNA library. / Hedayati, Poya; Monfard, Hossein Hosseni; Md Isa, Nurulhikma; Hwang, Duk Ju; Che Mohd. Zain, Che Radziah; Uddin, Md Imtiaz; Zuraida, Ab Rahman; Ismail, Ismanizan; Zainal, Zamri.

In: Acta Physiologiae Plantarum, Vol. 37, No. 5, 01.05.2015.

Research output: Contribution to journalArticle

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AU - Che Mohd. Zain, Che Radziah

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