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Title

Identification of putative drought-responsive genes in rice using gene co-expression analysis

 

Authors

Yanmei Lv1,#, Lei Xu2,#, Komivi Dossa3, Kun Zhou1, Mingdong Zhu1, Hongjun Xie1, Shanjun Tang1, Yaying Yu1, Xiayu Guo4,*, Bin Zhou1,5,*

 

Affiliation

1Hunan Rice Research Institute, Changsha, 410125, China; 2College of Pharmacy, Hubei University of Chinese Medicine, China; 3Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China; 4State key laboratory of hybrid rice, Changsha, 410125, China; 5Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture, Changsha, 410125, China; #Equal contribution

 

Email

Komivi Dossa - E-mail: komiri.dossa@ucad.edu.sn;

Xiayu Guo - E-mail: wanilybaobao@163.com;

Bin Zhou - zhoubin750517@163.com; *Corresponding author

 

Article Type

Research Article

 

Date

Received July 1, 2019; Accepted July 4, 2019; Published July 31, 2019

 

Abstract

Drought is one of the major abiotic stresses causing yield losses and restricted growing area for several major crops. Rice being a major staple food crop and sensitive to water-deficit conditions bears heavy yield losses due to drought stress. To breed drought tolerant rice cultivars, it is of interest to understand the mechanisms of drought tolerance. In this regard, large amount of publicly available transcriptome datasets could be utilized. In this study, we used different transcriptome datasets obtained under drought stress in comparison to normal conditions (control) to identify novel drought responsive genes and their underlying molecular mechanisms. We found 517 core drought responsive differentially expressed genes (DEGs) and different modules using gene co-expression analysis to specifically predict their biological roles in drought tolerance. Gene ontology and KEGG analyses showed key biological processes and metabolic pathways involved in drought tolerance. Further, network analysis pinpointed important hub DEGs and major transcription factors regulating the expression of drought responsive genes in each module. These identified novel DEGs and transcription factors could be functionally characterized using systems biology approaches, which can significantly enhance our knowledge about the molecular mechanisms of drought tolerance in rice.

 

Keywords

drought; transcriptome; WGCNA; co-expressed genes; network analysis

 

Citation

Lv et al. Bioinformation 15(7): 480-488 (2019)

 

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.