Abstract
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.
Highlights
Rice (Oryza sativa) is one of the major food crops for more than 3.5 billion population of the world
Differentially expressed genes (DEG) between tolerant and susceptible varieties under salt and drought stress: Salt tolerant (CSR11) and salt sensitive (VSR156) rice varieties were grown under normal growth conditions and 14-day-old seedlings were exposed to salt stress (150mM NaCl) for 24 hrs
Drought tolerant (Vandana) and drought sensitive (IR64) rice varieties were grown under control and 14day-old seedlings were exposed to drought stress (12 hrs) conditions
Summary
Rice (Oryza sativa) is one of the major food crops for more than 3.5 billion population of the world. It was estimated that for an additional 1 billion population, 100 million additional tons of rice would be required but with limited resources. Rice is largely grown under rain fed condition [1] and often subjected to various types of abiotic stresses such as salinity [2, 3] and drought [4]. In India, 9.04 million hectare of rice growing area is affected by salinity leading to considerable loss of grain yield. Salinity stress but frequently occurred severe droughts drastically affect rice production [5]. Salinity and drought stresses causes osmotic imbalance on plants. There are several studies that have shown extensive cross talk between different abiotic
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