Abstract
Host specific resistance and non-host resistance are two plant immune responses to counter pathogen invasion. Gene network organizing principles leading to quantitative differences in resistant and susceptible host during host specific resistance are poorly understood. Vascular wilt caused by root pathogen Fusarium species is complex and governed by host specific resistance in crop plants, including chickpea. Here, we temporally profiled two contrasting chickpea genotypes in disease and immune state to better understand gene expression switches in host specific resistance. Integrative gene-regulatory network elucidated tangible insight into interaction coordinators leading to pathway determination governing distinct (disease or immune) phenotypes. Global network analysis identified five major hubs with 389 co-regulated genes. Functional enrichment revealed immunome containing three subnetworks involving CTI, PTI and ETI and wilt diseasome encompassing four subnetworks highlighting pathogen perception, penetration, colonization and disease establishment. These subnetworks likely represent key components that coordinate various biological processes favouring defence or disease. Furthermore, we identified core 76 disease/immunity related genes through subcellular analysis. Our regularized network with robust statistical assessment captured known and unexpected gene interaction, candidate novel regulators as future biomarkers and first time showed system-wide quantitative architecture corresponding to genotypic characteristics in wilt landscape.
Highlights
Plants frequently encounters to wide range of patho-stresses that modulate growth and development thereby affecting the overall productivity
To investigate genotype specific cellular responses during host specific resistance, we screened different chickpea varieties challenged with Fusarium oxysporum
Compared to other methods of differential gene expression analyses[60], the major advantage of our strategy is that the gene is included in the network based on prior evidence narrowing the assumption based conclusions of interactions between candidate genes and at the same platform discover novel candidate with known interactions
Summary
Plants frequently encounters to wide range of patho-stresses that modulate growth and development thereby affecting the overall productivity. Transcript profiling assist in elucidating logic of regulatory circuits to provide insights into cellular processes and identification of interaction architecture to manage plant immune response[30]. We present integrative functional network analyses based on cDNA microarray temporal datasets consisting of 6072 spots representing 1749 unigenes to examine the common and discrete features of chickpea gene network during host specific resistance in response to Fusarium wilt. We assembled gene network by integrating temporal gene expression data from two contrasting chickpea genotypes differing in patho-stress response. A diseasome and immunome was constructed to reveal invasion or resistance mechanism Corollary of this hypothesis was elucidated in unbiased manner to determine significant difference in gene expression and interdependencies among cellular components to determine relationships among variables. The study underpins genotype dependent transcriptional regulation during patho-stress and highlights the importance of module coordination in host specific plant defense
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