Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.

Dwijesh Chandra Mishra,M S Farooqi,Anuj Kumar,Devender Arora,Sudhir Srivastava,P S Pandey,K K Chaturvedi,S V Amitha Cr Mithra,Amolkumar U Solanke,Sanjeev Kumar,S B Lal,Neeraj Budhlakoti,Anil Rai

doi:10.3389/fgene.2021.780599

Abstract

Rice is an important staple food grain consumed by most of the population around the world. With climate and environmental changes, rice has undergone a tremendous stress state which has impacted crop production and productivity. Plant growth hormones are essential component that controls the overall outcome of the growth and development of the plant. Cytokinin is a hormone that plays an important role in plant immunity and defense systems. Trans-zeatin is an active form of cytokinin that can affect plant growth which is mediated by a multi-step two-component phosphorelay system that has different roles in various developmental stages. Systems biology is an approach for pathway analysis to trans-zeatin treated rice that could provide a deep understanding of different molecules associated with them. In this study, we have used a weighted gene co-expression network analysis method to identify the functional modules and hub genes involved in the cytokinin pathway. We have identified nine functional modules comprising of different hub genes which contribute to the cytokinin signaling route. The biological significance of these identified hub genes has been tested by applying well-proven statistical techniques to establish the association with the experimentally validated QTLs and annotated by the DAVID server. The establishment of key genes in different pathways has been confirmed. These results will be useful to design new stress-resistant cultivars which can provide sustainable yield in stress-specific conditions.

Highlights

Rice (Oryza sativa) is an important food grain crop that is consumed worldwide (Kubo and Purevdorj, 2004)
In the process of finding the association of these genes with the well-known Quantitative trait locus (QTL) related to salt, cold, drought, bacterial stress, we found that 17 out of the 36 identified hub genes were associated with these QTLs mapped on various chromosomes (Figure 8)
To develop a variety that is resistant to these stresses, there is an urgent need to identify important hub genes governing the whole production process

Summary

Introduction

Rice (Oryza sativa) is an important food grain crop that is consumed worldwide (Kubo and Purevdorj, 2004). Plants must be able to react rapidly with various abiotic and biotic stress signals and develop efficient defense responses to cope with adverse conditions arising in the field (Kumar et al, 2015). Cytokinin pathway has been widely studied and a huge amount of gene expression data are available in public repositories (Edgar et al, 2002; Leinonen et al, 2011) These data can be better utilized for constructing gene regulatory networks and identifying key genes which will further help in developing improved rice varieties having the ability to produce high yield and resistance to such abiotic stress and adverse conditions (Stuart et al, 2003; Lelandais et al, 2011)

Methods

Results

Conclusion