A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice

Juexin Wang,Dong Xu,Yan Wang,Yanchun Liang,Ying Xu,Liang Chen,Jingfen Zhang

doi:10.1371/journal.pone.0064929

Juexin Wang, Dong Xu + Show 5 more

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https://doi.org/10.1371/journal.pone.0064929

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Abstract

Salinity is one of the most common abiotic stresses in agriculture production. Salt tolerance of rice (Oryza sativa) is an important trait controlled by various genes. The mechanism of rice salt tolerance, currently with limited understanding, is of great interest to molecular breeding in improving grain yield. In this study, a gene regulatory network of rice salt tolerance is constructed using a systems biology approach with a number of novel computational methods. We developed an improved volcano plot method in conjunction with a new machine-learning method for gene selection based on gene expression data and applied the method to choose genes related to salt tolerance in rice. The results were then assessed by quantitative trait loci (QTL), co-expression and regulatory binding motif analysis. The selected genes were constructed into a number of network modules based on predicted protein interactions including modules of phosphorylation activity, ubiquity activity, and several proteinase activities such as peroxidase, aspartic proteinase, glucosyltransferase, and flavonol synthase. All of these discovered modules are related to the salt tolerance mechanism of signal transduction, ion pump, abscisic acid mediation, reactive oxygen species scavenging and ion sequestration. We also predicted the three-dimensional structures of some crucial proteins related to the salt tolerance QTL for understanding the roles of these proteins in the network. Our computational study sheds some new light on the mechanism of salt tolerance and provides a systems biology pipeline for studying plant traits in general.

Highlights

Salinity is one of agriculture’s most crucial problems in large parts of the world [1]
The oxidoreductase activity may be related to reactive oxygen intermediates (ROI) that are produced in response to oxidative stress due to a water deficit during salinity stress [14]
The increased oxidoreductase activity is consistent with known activation of the antioxidative enzymes such as catalase (CAT), ascorbate peroxidase (APX), guaicol peroxidase (POD), glutathione reductase (GR), and superoxide dismutase (SOD) under salt stress in plants [16]

Summary

Introduction

Salinity is one of agriculture’s most crucial problems in large parts of the world [1]. Rice (Oryza sativa L.), which provides a major food source for about half of the global population, is considered as the most important cereal crop in agriculture, but it is salt susceptible [2]. Under the heavy pressure of global population explosion and global climate change, studying rice salt tolerance is of high importance. Genetic improvements leading to salt tolerance of cereal crops in molecular breeding could help maintain stable global food supply [5]. Some traditional cultivars and landraces have been identified as tolerant to abiotic stresses, despite their undesirable agronomic traits such as tall plant stature, photosensitivity, poor grain quality and low yield. Pokkali, an Indian landrace, can maintain high K+/Na+ ratio in shoot in a high salinity environment, and it could be a donor of salt-tolerance strains in breeding programs. FL478 is an improved indica cultivar used as a salt-susceptibility standard [6]

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