Identification of Arabidopsis Candidate Genes in Response to Biotic and Abiotic Stresses Using Comparative Microarrays

Abstract

Plants have evolved with intricate mechanisms to cope with multiple environmental stresses. To adapt with biotic and abiotic stresses, plant responses involve changes at the cellular and molecular levels. The current study was designed to investigate the effects of combinations of different environmental stresses on the transcriptome level of Arabidopsis genome using public microarray databases. We investigated the role of cyclopentenones in mediating plant responses to environmental stress through TGA (TGACG motif-binding factor) transcription factor, independently from jasmonic acid. Candidate genes were identified by comparing plants inoculated with Botrytis cinerea or treated with heat, salt or osmotic stress with non-inoculated or non-treated tissues. About 2.5% heat-, 19% salinity- and 41% osmotic stress-induced genes were commonly upregulated by B. cinerea-treatment; and 7.6%, 19% and 48% of genes were commonly downregulated by B. cinerea-treatment, respectively. Our results indicate that plant responses to biotic and abiotic stresses are mediated by several common regulatory genes. Comparisons between transcriptome data from Arabidopsis stressed-plants support our hypothesis that some molecular and biological processes involved in biotic and abiotic stress response are conserved. Thirteen of the common regulated genes to abiotic and biotic stresses were studied in detail to determine their role in plant resistance to B. cinerea. Moreover, a T-DNA insertion mutant of the Responsive to Dehydration gene (rd20), encoding for a member of the caleosin (lipid surface protein) family, showed an enhanced sensitivity to B. cinerea infection and drought. Overall, the overlapping of plant responses to abiotic and biotic stresses, coupled with the sensitivity of the rd20 mutant, may provide new interesting programs for increased plant resistance to multiple environmental stresses, and ultimately increases its chances to survive. Future research directions towards a better dissection of the potential crosstalk between B. cinerea, abiotic stress, and oxylipin signaling are of our particular interest.

‘Omics’ and Plant Responses to Botrytis cinerea

“…Generally, transcriptomic measures are best suited for early identification of cell responses to an individual or multiple stress(es). Plant responses to B. cinerea undergo transcriptional reprograming, showing that over 12% of the Arabidopsis genome are differentially expressed genes (DEGs), of which 1498 (7%) and 1138 (5%) were reported to be B. cinerea -induced and -repressed genes, respectively (Sham et al, 2014, 2015). A number of DEGs, which were shown to be implicated in B. cinerea defense, encode transcription factors, including WRKYs (Birkenbihl et al, 2012; Liu et al, 2015), APETALA2/ethylene response factors (AP2/ERFs) (Son et al, 2012; Maruyama et al, 2013), TGAs (Windram et al, 2012; Sham et al, 2014), NACs (Wang et al, 2009), and MYBs (Ramírez et al, 2011).…”

“…A number of DEGs, which were shown to be implicated in B. cinerea defense, encode transcription factors, including WRKYs (Birkenbihl et al, 2012; Liu et al, 2015), APETALA2/ethylene response factors (AP2/ERFs) (Son et al, 2012; Maruyama et al, 2013), TGAs (Windram et al, 2012; Sham et al, 2014), NACs (Wang et al, 2009), and MYBs (Ramírez et al, 2011). Several studies focusing on the transcriptional regulation of responses to multiple stresses have identified commonly regulated genes responsive to both B. cinerea infection and simultaneous abiotic stresses, such as drought, heat, or salinity, in Arabidopsis using microarray analyses (Atkinson and Urwin, 2012; Sham et al, 2015). In tomato, a transcriptomic study using RNAseq has distinguished the natural variation among wild Solanum species (Smith et al, 2014).…”

“…Transcriptomics enables us to identify potential candidate genes functioning in plant defense, whereas mutant lines with knockout and/or overexpression traits allow us to elucidate their function in the defense response. Botrytis-induced kinase 1 ( BIK1 ), responsive to dehydration 20 ( RD20 ), pentatricopeptide repeat protein for germination on NaCl ( PGN ), and expansin-like A2 ( EXLA2 ) were identified as B. cinerea -responsive genes, and their mutants exhibited altered susceptibility to necrotrophic pathogens (Veronese et al, 2006; Laluk et al, 2011; AbuQamar et al, 2013; AbuQamar, 2014; Sham et al, 2015). Moreover, the Mediator 18 ( MED18 ), identified using RNAseq, was shown to modulate plant immunity and responses to hormones (Lai et al, 2014).…”

Genetic approaches to study plant responses to environmental stresses

“…For example, comparative genomic hybridization (CGH) microarrays allow the study of entire genomes to reveal DNA variations between genomes. Recently, transcriptome analyses to study plant responses to different environmental stresses have been reported in response to biotic and abiotic stresses [61,62], cold [63][64][65], drought [66][67][68], salt [69], and heat [70,71]. Figure 1 illustrates the general principle of key microarray methods.…”

Arabidopsis Transcriptome Changes Prior and Post Environmental Stresses

“…6,7 In the latter studies, the combinations of the expression of B. cinerea-upregulated genes (BUGs) and B. cinerea-downregulated genes (BDGs) with each of the six classes of environmental stresses were analyzed. It was found that 2.5%, 6%, 12%, 19%, 25% or 41% of the BUGs were also induced by heat, drought, oxidative stress, salinity, cold or osmotic stress, respectively.…”