Title

Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice
from co-expressed gene interaction networks

Authors

Pragya Mishra^1,2, Nisha Singh¹, Ajay Jain¹, Neha Jain¹, Vagish Mishra¹, Pushplatha G¹, Kiran P.
Sandhya³, Nagendra Kumar Singh¹, Vandna Rai^1*

Affiliation

¹National Research Centre on Plant Biotechnology, Indian Agriculture Research Institute, New Delhi, India, India;

²Banasthali University, Tonk, Rajasthan;

³Ocimum Biosolutions, Hyderabad, India;

Email

vandnarai2006@gmail.com;

Article Type

Hypothesis

Date

Received September 25, 2017; Revised September 28, 2017; Accepted October 30, 2017; Published March 31, 2018

Rice, a staple food crop, is often subjected to drought and salinity stresses thereby limiting its yield potential. Since there is a cross talk between these abiotic stresses, identification of common and/or overlapping regulatory elements is pivotal for generating rice cultivars that showed tolerance towards them. Analysis of the gene interaction network (GIN) facilitates identifying the role of individual genes and their interactions with others that constitute important molecular determinants in sensing and signaling cascade governing drought and/or salinity stresses. Identification of the various cis-regulatory elements of the genes constituting GIN is equally important. Here, in this study graphical Gaussian model (GGM) was used for generating GIN for an array of genes that were differentially regulated during salinity and/or drought stresses to contrasting rice cultivars (salt-tolerant [CSR11], salt-sensitive [VSR156], drought-tolerant [Vandana], drought-sensitive [IR64]). Whole genome transcriptom profiling by using microarray were employed in this study. Markov Chain completed co-expression analyses of differentially expressed genes using Dynamic Bayesian Network, Probabilistic Boolean Network and Steady State Analysis. A compact GIN was identified for commonly co-expressed genes during salinity and drought stresses with three major hubs constituted by Myb2 transcription factor (TF), phosphoglycerate kinase and heat shock protein (Hsp). The analysis suggested a pivotal role of these genes in salinity and/or drought stress responses. Further, analysis of cis-regulatory elements (CREs) of commonly differentially expressed genes during salinity and drought stresses revealed the presence of 20 different motifs.

Keywords

cis-regulatory elements, drought stress, gene interaction network, microarray, rice, salt stress

Citation

Mishra et al. Bioinformation 14(3): 123-131 (2018)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.