Abstract
Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice.
Highlights
Drought is a major environmental stress factor that affects the growth and development of plants
To determine a biologically relevant correlation coefficient for gene co-expression, we examined the changes in the actual number of edges in the co-expression network and all possible edges in the control network consisting of these non-singleton nodes as a function of r cutoff values
Expression analysis showed that these genes, including HSF, were induced by drought stress and abscisic acid (ABA); their expression patterns exhibited obvious coherence in IRAT109 seedlings under PEG and ABA treatments (Figure 7B). These results suggest that the ABA-responsive element (ABRE) element is probably recognized by the HSF and these co-expression genes may be involved in the ABA-dependent drought response pathway in different rice varieties
Summary
Drought is a major environmental stress factor that affects the growth and development of plants. Plant drought stress response is one of the most complex biological processes, and it involves numerous changes at the physiological, cellular, and molecular levels. The current challenge for understanding the drought stress response is to discover the relationships between genes at a system-based level that leads to the formation of this complex process in plants. The gene co-expression network, which is one type of biological network, is constructed from microarray datasets that facilitate a global view of transcriptional relationships. This can help in the understanding of how genes interplay to carry out specific biological functions
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