Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

Abstract

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination

“…For example, WRKY is from a group of transcription factors that play a vital role in stress tolerance. Their expression was higher in Rt than in St, and similar results were obtained by other researchers who found contrasting expression pattern of genes like WRKY in resistant and susceptible genotypes [ 49 , 50 ]. These genes do not work independently, as shown in the metabolic pathway (Fig.…”

Application of Multilayer Network Models in Bioinformatics

“…Corresponding network structures for different biological data and specific subjects can also be designed to analyse specific biological systems ( Zeng et al, 2016 ; Jiang et al, 2017 ; Liu et al, 2017 ). Currently, at the subcellular level, these networks mainly include gene regulatory networks ( Wang et al, 2010 ; Ding et al, 2011 ; Jiang et al, 2014 ; Cheng et al, 2019 ; Konda et al, 2019 ; Liu L. et al, 2019 ; Mortezaeefar et al, 2019 ; Hong et al, 2020 ), protein functional networks ( Guo et al, 2011 , 2013 , 2014 ; Sikandar et al, 2019 ; Tao et al, 2020 ; Liu et al, 2021 ), metabolic regulatory networks ( Jin et al, 2020 ), and drug targeting networks ( Wei et al, 2014 ; Ding et al, 2017 , 2019 , 2020a , b ; Jin Q. et al, 2019 ; Jin S. et al, 2019 ; Srivastava et al, 2019 ; Zhao et al, 2019 ; Zeng et al, 2020 ).…”