Planta

, Volume 238, Issue 4, pp 669–681

Genome-wide expression analysis of rice aquaporin genes and development of a functional gene network mediated by aquaporin expression in roots

Original Article

DOI: 10.1007/s00425-013-1918-9

Cite this article as:
Nguyen, M.X., Moon, S. & Jung, K. Planta (2013) 238: 669. doi:10.1007/s00425-013-1918-9

Abstract

The world population continually faces challenges of water scarcity for agriculture. A common strategy called water-balance control has evolved to adapt plant growth to these challenges. Aquaporins are a family of integral membrane proteins that play a central role in water-balance control. In this study, we identified 34 members of the rice aquaporin gene family, adding a novel member to the previous list. A combination of phylogenetic tree and anatomical meta-expression profiling data consisting of 983 Affymetrix arrays and 209 Agilent 44 K arrays was used to identify tissue-preferred aquaporin genes and evaluate functional redundancy among aquaporin family members. Eight aquaporins showed root-preferred expression in the vegetative growth stage, while 4 showed leaf/shoot-preferred expression. Integrating stress-induced expression patterns into phylogenetic tree and semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) analyses revealed that 3 rice aquaporin genes were markedly downregulated and 4 were upregulated by water deficiency in the root, suggesting that these candidate genes are key regulators of water uptake from the soil. Finally, we constructed a functional network of genes mediated by water stress and refined the network by confirming the differential expression using RT-PCR and real-time PCR. Our data will be useful to elucidate the molecular mechanism of water-balance control in rice root.

Keywords

Drought stress in rootFunctional gene networkGene redundancyMeta-profiling analysis

Abbreviations

AQP

Aquaporin

D

Day(s)

IDs

Identifiers

H

Hour(s)

Lsi

Low silicon rice

MEGA

Molecular evolutionary genetics analysis

Min

Minute(s)

NIPs

Nodulin 26-like intrinsic proteins

NPA

Asparagine–proline–alanine region

PIPs

Plasma membrane intrinsic proteins

qRT-PCR

Semi-quantitative reverse transcription polymerase chain reaction

RGAP

Rice genome annotation project database

RWC

Rice water channel

SAM

Shoot apical meristem

S

Second(s)

SIPs

Small basic intrinsic proteins

TIPs

Tonoplast intrinsic proteins

XIPs

Uncategorized X intrinsic proteins

Supplementary material

425_2013_1918_MOESM1_ESM.jpg (1.3 mb)
Fig. S1 Chromosomal distribution of 34 rice aquaporin genes. Red boxes denote a new member (JPEG 1311 kb)
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Fig. S2 The phylogenetic tree of rice aquaporin proteins (JPEG 1231 kb)
425_2013_1918_MOESM3_ESM.eps (3.7 mb)
Fig. S3 The phylogenomic data of the rice aquaporins with orthologs from Arabidopsis and maize (EPS 3828 kb)
425_2013_1918_MOESM4_ESM.jpg (1.6 mb)
Fig. S4 Anatomical expression of rice aquaporin genes using 1150 Affymetrix and 209 Agilent 44 K arrays. A black bar denotes an indica cultivar and a grey bar a japonica cultivar (JPEG 1598 kb)
425_2013_1918_MOESM5_ESM.xlsx (13 kb)
Table S1 Detailed information for 34 rice aquaporin genes (XLSX 12 kb)
425_2013_1918_MOESM6_ESM.docx (19 kb)
Table S2 Primer sequences for RT-PCR and real-time PCR of aquaporin genes and genes functionally associated with aquaporins, used in Figs. 2, 4, and 5 (DOCX 19 kb)
425_2013_1918_MOESM7_ESM.xlsx (34 kb)
Table S3 Detailed comparison of microarrays used for Fig. 3 (XLSX 34 kb)

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of Plant Molecular Systems Biotechnology and Crop Biotech InstituteKyung Hee UniversityYonginKorea