Functional & Integrative Genomics

, Volume 9, Issue 3, pp 411–417

Histidine kinase and response regulator genes as they relate to salinity tolerance in rice

  • Ratna Karan
  • Sneh L. Singla-Pareek
  • Ashwani Pareek
Short Communication

DOI: 10.1007/s10142-009-0119-x

Cite this article as:
Karan, R., Singla-Pareek, S.L. & Pareek, A. Funct Integr Genomics (2009) 9: 411. doi:10.1007/s10142-009-0119-x

Abstract

We have previously shown that Oryza sativa L. Pokkali maintains higher levels of transcripts under non-saline conditions, which are otherwise induced under salinity in the sensitive genotype—IR64. We wanted to test this hypothesis of differential gene regulation further, within the members of a given stress responsive gene family, which share significant structural and functional similarities. For this purpose, we chose to work on the two-component system (TCS family) which plays an important role in stress perception and signal transduction under hormonal, abiotic stress, light and developmental regulation. We present data to show that all members of TCS family, including sensory histidine kinases, phosphotransfer proteins and response regulators, are having differential transcript abundance (under both non-stress and salinity stress conditions) in contrasting rice genotypes. Further, under non-stress conditions, transcript abundance for all TCS members (except RR21) was found to be higher in the salt-tolerant genotype—Pokkali. TCS transcripts are otherwise induced by salinity stress to a relatively higher level in the sensitive cultivar IR64. A few of these members were also found to be localised within important salinity-related quantitative trait loci identified earlier. Based on the above findings, we propose that the TCS members may have a significant role in salinity tolerance in rice and can serve as useful ‘candidate genes’ for raising salinity-tolerant crop plants.

Keywords

Contrasting genotypes Histidine kinase Oryza sativa L. Salinity Two-component system QTLs 

Abbreviations

TCS

Two-component system

HK

Histidine kinase

HPT

Phosphotransfer protein

RR

Response regulator

QTL

Quantitative trait loci

RFLP

Restriction fragment length polymorphism

Supplementary material

10142_2009_119_Fig1_ESM.gif (64 kb)
SUPPL Fig. 1

qRT-PCR analysis of TCS genes in contrasting rice genotypes under non-stress conditions. a Cartoon depicting the functioning of a hybrid type histidine kinase (TCS system) in eukaryotes. b Analysis of sensory HK genes expressed under non-stress conditions. c Analysis of HPT genes expressed under non-stress conditions. d Analysis of RR genes expressed under non-stress conditions. The values represented in each sample are the mean of two biological and three technical replicates, whilst bars indicate the standard error of triplicates. The expression of each TCS gene in control RNA samples of IR64 and Pokkali was normalised with the expression of internal control gene, actin (GIF 64.2 KB).

10142_2009_119_MOESM2_ESM.tif (644 kb)
High resolution image file (TIFF 643 KB).
10142_2009_119_Fig2_ESM.gif (51 kb)
SUPPL Fig. 2

Fold increase of TCS transcripts in two contrasting genotypes of rice under salinity stress. a Fold change of sensory HK genes expressed during salinity stress condition by qRT-PCR. b Fold change of HPT genes expressed during salinity stress condition. c Fold change of RR genes differentially expressed during salinity stress condition. The mRNA levels for each gene in seedlings subjected to salinity stress were calculated relative to its expression in control seedlings using ΔΔCT method. The values represented are the mean of two biological and three technical replicates, whilst bars indicate the standard error of triplicates. The expression of each gene in the RNA samples was normalised with the expression of the internal control gene, actin (GIF 50.5KB).

10142_2009_119_MOESM4_ESM.tif (536 kb)
High resolution image file (TIFF 563 KB).
10142_2009_119_Fig3_ESM.gif (84 kb)
SUPPL Fig. 3

Heat map display of TCS genes under control and salinity stress conditions in two contrasting genotypes of rice. a Heat map of sensory HKs, b heat map of HPTs and c heat map of RRs. IRC IR64 control, IRS salinity-stressed IR64, POKC Pokkali control, POKS salinity-stressed Pokkali. Normalised CT value of each sample with respect to actin was used for Heat map analysis (GIF 83.5 KB).

10142_2009_119_MOESM6_ESM.tif (5.6 mb)
High resolution image file (TIFF 5.63 MB).
10142_2009_119_Fig4_ESM.gif (12 kb)
SUPPL Fig. 4

Histogram showing the distribution of sensory HKs, HPTs and RRs on various rice chromosomes (GIF 12.0 KB).

10142_2009_119_MOESM8_ESM.tif (259 kb)
High resolution image file (TIFF 258 KB).

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Ratna Karan
    • 1
  • Sneh L. Singla-Pareek
    • 2
  • Ashwani Pareek
    • 1
  1. 1.Stress Physiology and Molecular Biology, School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
  2. 2.Plant Molecular BiologyInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia

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