Abstract
A wide range of biotic stresses (BS) and abiotic stresses (AS) adversely affect plant growth and productivity worldwide. The study of individual genes cannot be considered as an effective approach for the understanding of tolerance mechanisms, since these stresses are frequent and often in combination with each other, and a large number of genes are involved in these mechanisms. The availability of high-throughput genomic data has enabled the discovery of the role of transcription factors (TFs) in regulatory networks. A meta-analysis of BS and AS responses was performed by analyzing a total of 391 microarray samples from 23 different experiments and 2,336 differentially expressed genes (DEGs) involved in multiple stresses were identified. We identified 1,862 genes differentially regulated in response to BS was much greater than that regulated by AS, 835 genes, and found 15.4% or 361 DEGs with the conserved expression between AS and BS. The greatest percent of genes related to the cellular process (>76% genes), metabolic process (>76% genes) and response to stimulus (>50%). About 4.2% of genes involved in BS and AS responses belonged to the TF families. We identified several genes, which encode TFs that play an important role in AS and BS responses. These proteins included Jasmonate Ethylene Response Factor 1 (JERF1), SlGRAS6, MYB48, SlERF4, EIL2, protein LATE ELONGATED HYPOCOTYL (LHY), SlERF1, WRKY 26, basic leucine zipper TF, inducer of CBF expression 1-like, pti6, EIL3 and WRKY 11. Six of these proteins, JERF1, MYB48, protein LHY, EIL3, EIL2 and SlGRAS6, play central roles in these mechanisms. This research promoted a new approach to clarify the expression profiles of various genes under different conditions in plants, detected common genes from differentially regulated in response to these conditions and introduced them as candidate genes for improving plant tolerance through genetic engineering approach.
Highlights
As sessile organisms, plants constantly encounter a wide range of stresses that negatively affect the yield production, survival and growth of plants worldwide (Sharma et al, 2013)
Since transcription factors (TFs) are the key regulators of plant growth, development and metabolisms via up- and down-regulation of various genes, identification of the genes encoding these proteins and transferring them into plants to improve their stress tolerance would be interesting. These TFs (JERF1, Pti6, SlERF1, SlERF4, SlGRAS6, MYB48, protein LATE ELONGATED HYPOCOTYL (LHY), EIL2, EIL3, WRKY 11, WRKY 26, inducer of CBF expression 1 (ICE1)-like and bZIP TF) can be used as candidate genes in molecular breeding programs because these TFs are common to abiotic stresses (AS) and biotic stresses (BS); our results indicate they are being affected by a wide range of stresses
We identified 1,862 and 835 genes differentially regulated in response to BS and AS, respectively, and 361 genes identified in this work are to be involved in cross-talk between BS and AS responses
Summary
Plants constantly encounter a wide range of stresses that negatively affect the yield production, survival and growth of plants worldwide (Sharma et al, 2013). To survive under stress conditions, complex mechanisms have evolved in plants to perceive signals from their environment, transmit through signal transduction pathways and respond to the various stresses that each of which may involve several hundred proteins (Fujita et al, 2006; Rastgoo, Alemzadeh & Afsharifar, 2011; Atkinson, Lilley & Urwin, 2013; Sharma et al, 2013; Sami & Alemzadeh, 2016). TFs are proteins with critical roles in the control temporal and spatial gene expression during defense response that many of them are induced by more than one stress (Berrocal-Lobo, Molina & Solano, 2002; Liu et al, 2014; Shaik & Ramakrishna, 2014; Prasad et al, 2016)
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