Abstract
Drought alone or in combination with other stresses forms the major crop production constraint worldwide. Sorghum, one of the most important cereal crops is affected by drought alone or in combination with co-occurring stresses; notwithstanding, sorghum has evolved adaptive responses to combined stresses. Furthermore, an impressive number of sorghum genes have been investigated for drought tolerance. However, the molecular mechanism underling drought response remains poorly understood. We employed a systems biology approach to elucidate regulatory and broad functional features of these genes. Their interaction network would provide insight into understanding the molecular mechanisms of drought tolerance and underpinning signal pathways. Functional analysis was undertaken to determine significantly enriched genesets for pathways involved in drought tolerance. Analysis of distinct pathway cross-talk network was performed and drought-specific subnetwork was extracted. Investigation of various data sources such as gene expression, regulatory pathways, sorghumCyc, sorghum protein-protein interaction (PPI) and Gene Ontology (GO) revealed 14 major drought stress related hub genes (DSRhub genes). Significantly enriched genesets have shown association with various biological processes underlying drought-related responses. Key metabolic pathways were significantly enriched in the drought-related genes. Systematic analysis of pathways cross-talk and gene interaction network revealed major cross-talk pathway modules associated with drought tolerance. Further investigation of the major DSRhub genes revealed distinct regulatory genes such as ZEP, NCED, AAO, and MCSU and CYP707A1. These were involved in the regulation of ABA biosynthesis and signal transduction. Other protein families, namely, aldehyde and alcohol dehydrogenases, mitogene activated protein kinases (MAPKs), and Ribulose-1,5-biphosphate carboxylase (RuBisCO) were shown to be involved in the drought-related responses. This shows a diversity of complex functional features in sorghum to respond to various abiotic stresses. Finally, we constructed a drought-specific subnetwork, characterized by unique candidate genes that were associated with DSRhub genes. According to our knowledge, this is the first in sorghum drought investigation that introduces pathway and network-based candidate gene approach for analysis of drought tolerance. We provide novel information about pathways cross-talk and signaling networks used in further systems level analysis for understanding the molecular mechanism behind drought tolerance and can, therefore, be adapted to other model and non-model crops.
Highlights
Drought is a natural hazard and devastating phenomenon that severely affects agriculture and human life more than any other abiotic stress (Ivits et al, 2014)
It was noted that this category was dominant to which a minimum of 50 drought stress related genes (DRGs) were classified in each sub-category
Based on the Gene Ontology (GO) enrichment analysis, several drought stress response related functional gene categories that were involved in abscisic acid (ABA) signal transduction, transcription regulation, stress response, hormones signal transduction, and ROS homeostasis were few among others identified (Table S1)
Summary
Drought is a natural hazard and devastating phenomenon that severely affects agriculture and human life more than any other abiotic stress (Ivits et al, 2014). While there are a number of other co-varying factors complicate the effect of drought, anthropogenic-induced changes of climate are considered to be the most important Factors, such as salinity, cold or heat stresses that usually co-exist with drought, play considerable role in compromising plant survival, and productions. As drought becomes sever following the intensity of heat due to increase in the temperature and change in the global climate, and as drought co-occurs with other stresses, investigation of genes, and traits for combined stress tolerance become more important. Drought and extreme temperature, salinity and heat frequently affect many agricultural sectors Such stress combination occurs in many regions around the globe and causes extreme agricultural losses by many folds than the damage caused by individual stress alone, these stresses usually are investigated separately (Suzuki et al, 2014). Drought stress with all the co-varying factors affect the plant life and productivity, and contribute to be a more confounded vulnerability risk of global food security
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