Multi-omics atlas of combinatorial abiotic stress responses in wheat

We present a transcriptomic atlas of abiotic stress tolerance in wheat. We employed a systems biology approach to study physiological, metabolomic and transcriptomic responses associated with heat, drought, salinity and their possible combinations. Our objectives were to (1) rank stress treatments based on the overall physiological and growth impacts, (2) identify the core sets of genes common to a particular stress type, (3) examine pathways that are uniquely expressed in the various stress combinations, (4) detect associations between phenotypic and transcriptomic responses, (5) suggest possible transcription factors for further characterization and use in improving wheat performance in multi-stress environments. Triticum aestivum cv. Stettler, a Canada Western Red Spring wheat variety, was selected for this study. To evaluate plant adjustments to sub-lethal stress and stress combinations, transcriptomic changes in flag leaves during grain filling were assessed. From spike initiation (Feekes scale stage 8) onwards, greenhouse potted Stettler plants were subjected to one of eight treatments: control (C), heat (H), drought (D), salinity (S), heat and drought (HD), salinity and heat (SH), salinity and drought (SD) and, lastly, a salinity, heat and drought (SHD) treatment. For transcriptome analysis, total RNA was extracted from flag leaf from at least four independent biological replicates per stress treatment, and was sequenced using Illumina platform, generating over a billion paired-end short reads. Filtered reads were aligned to the wheat reference genome (IWGSC v1.1) using STAR. Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and transcripts per million (TPM) values were generated.