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

Abstract

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.

Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

“…To further reveal the potential roles that AS may play in L. chinense , we performed WGCNA of the AS genes. As a powerful tool with which to reveal the relationships between different gene sets or between genes and phenotypes, WGCNA has been extensively applied in different fields, such as medicine and plant science ( Wang J.-L. et al., 2019 ; Zhu et al., 2019 ; Esmaeili et al., 2020 ; Jia et al., 2020 ). We found that pistils and leaves may have huge differences in transcription and post-transcriptional regulation, because most blue-module genes that were related to transcription and post-transcriptional regulation were strongly expressed in pistils but weakly expressed in leaves ( Figures 6A , S3A , and S4A ).…”

“…Genes from the same coexpression module usually have similar expression patterns and closely related functions ( Jia et al., 2020 ). Researchers can associate coexpression modules with different traits to reveal the relationships between gene sets and phenotypes, and this method had been widely applied in the fields of medicine and plant science ( Wang J.-L. et al., 2019 ; Zhu et al., 2019 ; Esmaeili et al., 2020 ; Jia et al., 2020 ). However, using WGCNA to reveal the AS gene coexpression module in L. chinense had not been reported.…”

Drought tolerance molecular responses of two cultivated varieties Jerusalem artichoke (Helianthus tuberosus L.) as revealed by RNA-Seq

“…The NAC transcription factor JUB1 in tomato is the drought-tolerant regulator of tomato. SlJUB1 controls the expression of SlDREB1, SlDREB2 and SlDLALA, while AtJUB1 in A. thaliana stimulates the expression of DREB2a and produces drought resistance by controlling the DREB genes [46,47]. DREB2 and DREB2a were also highly expressed in both varieties of Jerusalem artichoke, particularly in QY3, in which the expression of DREB2 was extremely high.…”

Transcriptome changes induced by drought stress in Jerusalem artichoke (Helianthus tuberosus L.) and weighted gene co-expression network analysis (WGCNA)

“…WGCNA is an effective method for co-expression network analysis, which can speci cally screen out coexpression modules with high biological signi cance to target traits. It has been proved to be an e cient data mining method in rice [45], Brassica rapa [46], and sun ower [47]. In this study, the WGCNA method was used to construct a weighted gene co-expression network based on the sequencing data of 28 drought stress transcriptomes of Jerusalem artichoke.…”