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Plant Molecular Biology

, Volume 77, Issue 1–2, pp 129–144 | Cite as

Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings

  • Yohei Nanjo
  • Kyonoshin Maruyama
  • Hiroshi Yasue
  • Kazuko Yamaguchi-Shinozaki
  • Kazuo Shinozaki
  • Setsuko Komatsu
Article

Abstract

To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings.

Keywords

Soybean Seedling Flooding Transcriptome 

Abbreviations

ACD

Accelerated cell death

AOC

Allene oxide cyclase

ARAF

Alpha-l-arabinofuranosidase

ASNS

Asparagine synthase

5AT

Anthocyanin 5-aromatic acyltransferase

COMT

Caffeic acid O-methyl transferase

CS

Citrate synthase

FIS

Flooding inducible gene encoding small protein

IDH

Isocitrate dehydrogenase

MAT

Anthocyanin malonyltransferase

MDH

Malate dehydrogenase

MLO

Mildew resistance locus O

NR

Nitrate reductase

PEPCase

Phosphoenolpyruvate carboxylase

PGM

Phosphoglucomutase

PK

Pyruvate kinase

PPFK

Phosphofructokinase

qRT–PCR

Quantitative RT–PCR

sORFs

Small open reading frames

SK1, 2

Snorkel 1, 2

Sub1A

Submergence 1A

Susy

Sucrose synthase

TCA

Tricarboxylic acid

TPI

Triose phosphate isomerase

TPP

Trehalose phosphate phosphatase

TPS

Trehalose phosphate synthase

UGPase

UDP-gluocse pyrophosphorylase

XLG

Extra-large G-protein

Notes

Acknowledgments

We thank Dr. N Ahsan, Mr. Nouri Mohammad Zaman, Dr. Takuji Nakamura, Dr. Keito Nishizawa, Dr. Satoshi Shimamura, and Dr. Ryo Yamamoto for their helpful discussions. This work was supported by a Grant-in-Aid for Scientific Research (B) (1980015) from the Japan Society for the Promotion of Science.

Supplementary material

11103_2011_9799_MOESM1_ESM.tif (470 kb)
Supplementary Figure S1. Verification of microarray results by quantitative RT-PCR. The qRT-PCR analyses were performed with 6- and 12-h flooding treated and untreated samples to assess the microarray data. The Log2FC values of nine genes calculated from the qRT-PCR data from three biological replicates were plotted against the microarray data. A, the microarray data (white circle) and qRT-PCR (black circle) data of each gene were plotted together. B, scatter plot of microarray data versus qRT-PCR. The correlation coefficient (R2) between the two datasets is 0.954. (TIFF 470 kb)
11103_2011_9799_MOESM2_ESM.tif (3.6 mb)
Supplementary Figure S2. Overview of transcriptional changes in metabolic pathway under flooding. Log2FC values of differentially expressed genes were analyzed by use of the MapMan software. The color of each square indicates the Log2FC value of each gene. (TIFF 3697 kb)
11103_2011_9799_MOESM3_ESM.tif (922 kb)
Supplementary Figure S3. Alignment of deduced amino acid sequences of the highly inducible genes. The sequences were aligned by MAFFT multiple alignment program ver.6 (Katoh and Toh, 2008). The alignment was visualized by Jalview program 2.6.1. (Waterhouse et al., 2009). (A) alignment of amino acid sequences of FIS1, FIS2 and FIS3. B, alignment of amino acid sequences of FIS1 and Glyma12g05200.1. © alignment of amino acid sequences of FIS2, FIS16, FIS35 and FIS60. Contrast of color of shaded text indicates percent of identity. (TIFF 922 kb)
11103_2011_9799_MOESM4_ESM.tif (990 kb)
Supplementary Figure S4. In situ hybridization analysis of untreated soybean seedlings using probes for flooding inducible three genes. Bars in cotyledon panels and other panels indicate 200 μm and 1000 μm, respectively. (TIFF 990 kb)
11103_2011_9799_MOESM5_ESM.tif (1.5 mb)
Supplementary Figure S5. Root-tip death of flooded soybean seedlings. (A) Three days old seedling. (B) Flooded seedlings. The 2 days old seedlings were flooded with water for 3 days. After the 3 days of flooding treatment, the seedlings were grown on sands with normal irrigation for 2 days. Arrows indicate the region where the cell death like necrosis was observed. Bars indicate 10 mm. (TIFF 1517 kb)
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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Yohei Nanjo
    • 1
  • Kyonoshin Maruyama
    • 2
  • Hiroshi Yasue
    • 3
    • 4
  • Kazuko Yamaguchi-Shinozaki
    • 2
    • 5
  • Kazuo Shinozaki
    • 6
  • Setsuko Komatsu
    • 1
  1. 1.National Institute of Crop ScienceTsukubaJapan
  2. 2.Biological Resources DivisionJapan International Research Center for Agricultural SciencesTsukubaJapan
  3. 3.Division of Animal ScienceNational Institute of Agricultural SciencesTsukubaJapan
  4. 4.Tsukuba GeneTechnology Laboratories Inc.TsukubaJapan
  5. 5.Graduate School of Agricultural and Life SciencesUniversity of TokyoTokyoJapan
  6. 6.Plant Science CenterRIKENYokohamaJapan

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