Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species

As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1andisopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors,AP2-EREBP,MADS-box,WRKY22,MYB,homoeboxgenes members were significantly modulated by drought stress whereas cold stress enhancedAP2-EREBPs,bZIPmembers,MYB7,BELL 1and onebHLHmember.C2C2-CO-LIKE,MADS-boxand ahomeobox(HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressedglutaredoxingenes. Cold stress mostly upregulatedMAP kinases(mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.

Automated summary

A meta-analysis was conducted to identify conserved genes across plant species involved in general abiotic stress conditions and specific stress factors in leaf tissues. Differential gene expression patterns were observed for different abiotic stresses, such as drought, heat, and cold, with certain genes showing consistent upregulation or downregulation in response to these stress factors. This study provides insights into the molecular mechanisms underlying plant responses to various abiotic stresses.