期刊论文详细信息
Genes
WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Peisong Hu1  Xiangjin Wei1  Yinghong Yu2  Yaying Yu3  Mingdong Zhu3  Jianlong Wang3  Suozhen Hui3  Hongjun Xie4  Guohua Tang4  Xiaoshan Zeng4  Komivi Dossa5 
[1] China National Rice Research Institute, Hangzhou 311401, China;Hunan Academy of Agricultural Sciences, Changsha 410125, China;Hunan Agricultural University, Changsha 410128, China;Hunan Rice Research Institute, Changsha 410125, China;Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China;
关键词: salt stress;    transcriptome;    weighted gene co-expression network analysis (WGCNA);    co-expressed genes;    network analysis;    rice;   
DOI  :  10.3390/genes10090719
来源: DOAJ
【 摘 要 】

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.

【 授权许可】

Unknown   

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