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Open AccessCommunication

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

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Hunan Agricultural University, Changsha 410128, China
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Hunan Rice Research Institute, Changsha 410125, China
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China National Rice Research Institute, Hangzhou 311401, China
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Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China
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Hunan Academy of Agricultural Sciences, Changsha 410125, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 719; https://doi.org/10.3390/genes10090719
Received: 19 August 2019 / Revised: 7 September 2019 / Accepted: 11 September 2019 / Published: 17 September 2019
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties. View Full-Text
Keywords: salt stress; transcriptome; weighted gene co-expression network analysis (WGCNA); co-expressed genes; network analysis; rice salt stress; transcriptome; weighted gene co-expression network analysis (WGCNA); co-expressed genes; network analysis; rice
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Zhu, M.; Xie, H.; Wei, X.; Dossa, K.; Yu, Y.; Hui, S.; Tang, G.; Zeng, X.; Yu, Y.; Hu, P.; Wang, J. WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice. Genes 2019, 10, 719.

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