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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
WGCNA analysis of salt-responsive core transcriptome identifies novel hub genes in rice
Genes, Volume 10, No. 9, Article 719, Year 2019
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Description
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. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
Authors & Co-Authors
Dossa, Komivi
China, Wuhan
Wuhan Benagen Tech Solutions Company Limited
Statistics
Citations: 48
Authors: 1
Affiliations: 3
Identifiers
Doi:
10.3390/genes10090719
ISSN:
20734425
Research Areas
Food Security
Genetics And Genomics
Noncommunicable Diseases
Study Approach
Systematic review