Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum (Sorghum bicolor (L.) Moench) Responses to Drought and It's Co-occurring Stresses

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.

Identification of Age-Specific and Common Key Regulatory Mechanisms Governing Eggshell Strength in Chicken Using Random Forests

“…In line with previous studies [39,42,[101][102][103], we applied a systems biology approach and identified master regulators to investigate and unravel the transcriptional regulatory machinery of ESS associated genes. Interestingly, our results show that, similar to the genes, there are common master regulators (Sox11 and Slc22a1) for both time points, which are likely to govern various eggshell related processes during the laying of the birds.…”

“…Recently, the use of systems biology based approaches to study the traits of economic importance is gaining importance in the field of agriculture [39,[102][103][104]. However, one of the major impediments in the use of this knowledge in practical animal breeding is to integrate this large amount of information into traditional genetic evaluation programs [105].…”

Identification of heat-tolerance QTLs and high-temperature stress-responsive genes through conventional QTL mapping, QTL-seq and RNA-seq in tomato

“…The number of specific heat-tolerance genes in currant tomato was higher than that in cultivated tomato, indicating that wild currant tomato had more HSR genes than cultivated tomato, and these genes may partly explain the molecular differences in heat tolerance between currant tomato and cultivated tomato. KEGG enrichment analysis showed that the processes of pentose and glucuronidate interconversions and plant hormone signal transduction , the MAPK signaling pathway , starch and sucrose metabolism , and fatty acid metabolism were significantly enriched under high-temperature stress, which has been confirmed to be related to the high-temperature stress response under high temperature, and plant hormone signal transduction and the MAPK signaling pathway are related to high-temperature stress signaling [45–48].…”

Genetic dissection of heat-responsive physiological traits to improve adaptation and increase yield potential in soft winter wheat

“…We also found MTAs associated with drought stress. Moreover, we found several other MTAs whose annotations suggest different roles including response to drought stress (TBC1 domain family member, SNF1-related protein kinase regulatory subunit beta-2) plant senescence (E3 ubiquitin-protein ligase ORTHRUS 2), salt stress (Glutamyl-tRNA (Gln) amidotransferase subunit A), disease resistance (Disease resistance protein (NBS-LRR class) family), metabolism (Adenosine kinase-like protein) and antioxidant defense (Telomere repeat-binding factor like-protein) [30][31][32][33][34][35][36]. Our study identified novel MTAs associated with SPAD measurements in US soft wheat under HT conditions which contributes to a better understanding of the genetic basis of SPAD traits in wheat.…”