Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.)

Abstract

SummaryPlant can acquire tolerance to environmental stresses via transcriptome reprogramming at transcriptional and alternative splicing (AS) levels. However, how AS coordinates with transcriptional regulation to contribute to abiotic stresses responses is still ambiguous. In this study, we performed genome‐wide analyses of AS responses to drought stress (DS), heat stress (HS) and their combination (HD) in wheat seedlings, and further compared them with transcriptional responses. In total, we found 200, 3576 and 4056 genes exhibiting significant AS pattern changes in response to DS, HS and HD, respectively, and combined drought and heat stress can induce specific AS compared with individual one. In addition, wheat homeologous genes exhibited differential AS responses under stress conditions that more AS events occurred on B subgenome than on A and D genomes. Comparison of genes regulated at AS and transcriptional levels showed that only 12% of DS‐induced AS genes were subjected to transcriptional regulation, whereas the proportion increased to ~40% under HS and HD. Functional enrichment analysis revealed that abiotic stress‐responsive pathways tended to be highly overrepresented among these overlapped genes under HS and HD. Thus, we proposed that transcriptional regulation may play a major role in response to DS, which coordinates with AS regulation to contribute to HS and HD tolerance in wheat.

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat

“…Previous studies have proven that transcriptional regulation and AS regulation are two parallel processes that function independently in the stress response with little overlap between target genes (Li et al ., ; Chang et al ., ; Ding et al ., ; Ling et al ., ; Liu et al ., ). In our analysis, we confirmed that transcriptional and AS regulation also affect distinct gene sets and biological processes, providing further evidence for their independent regulatory roles.…”

“…The HS‐responsive genes with AS regulation were defined based on the following criteria: (i) the highly expressed transcript set (FPKM ≥ 1.0 and all junction sites that were fully supported by Illumina reads) differed between the control and HS‐treated samples; (ii) for the highly expressed transcript (FPKM ≥ 1.0), the transcript expression percentage (transcript expression/the expression sum of all transcripts of the same gene) changed by more than 30% between the control and HS‐treated samples (Liu et al ., ), with supported Illumina read counts ≥5 for both samples, and the supported Illumina reads significantly differed (chi‐squared test, FDR‐corrected P ‐value <0.05) between the two samples.…”

“…Significantly, our recent study showed that some markers of the HS response (e.g., small heat shock proteins [sHSPs]) were highly upregulated after 10 min HS treatment in wheat (Wang et al ., 2017b), implying that more intensive studies involving the analysis of earlier HS treatment samples should be considered to uncover heat sensing and early signaling events. We also identified extensive alternative splicing (AS) events in HS‐response transcriptomes in wheat seedlings (Liu et al ., ), revealing the importance of post‐transcriptional regulation in HS adaptation in wheat. However, existing transcriptome analyses have been based on incomplete genome sequences, incomprehensive gene annotation, a lack of grain‐filling stage samples and fragmented genes assembled from second‐generation sequencing data (usually 100–150 base pairs [bp]), making it impossible to capture the global landscape of HS responses and adaptations in wheat.…”

Dehydration‐responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation‐mediated regulation of stress response

“…Abiotic stress‐mediated changes in splicing have recently been confirmed by several RNA‐seq analyses in plants. Whereas transcriptome profiling has highlighted shift in the expression and dominance of certain isoforms of splicing factors and splice variants accompanying stress response (Liu et al, ; Zhang et al, ), the mode of implementation of this regulation is far from clear. Increasing evidence suggest that ABA‐mediated response is mediated by pre‐mRNA splicing (Haak et al, ; Zhan et al, ).…”

Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant

“…For instance, during the development of seed, endosperm and embryo, the AS isoforms change significantly in maize [39]. In wheat, 251, 6618 and 7541 AS isoform changes were detected in response to drought stress, heat stress and combined stress in 9312 stress-responsive events, respectively [40]. But little is known about the number of AS changes in response to cold acclimation.…”