Abstract
Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.
Highlights
Water-deficit and heat are significant environmental threats that negatively impact crop production and quality, putting world food security at risk [1]
In Mediterranean conditions, such as those typically found across the Australian wheat belt, water-deficit stress usually starts during spring before anthesis, and water deficiency often continues to intensify through grain filling [8,9]
The novel miRNAs were newly discovered miRNAs in durum wheat
Summary
Water-deficit and heat are significant environmental threats that negatively impact crop production and quality, putting world food security at risk [1]. In our previous study [8], Australian genotypes with varying stress tolerance levels exhibited contrasting responses to water-deficit and heat stress— for yield components and for quality traits, such as grain protein content, and physiological traits, such as leaf chlorophyll content. This genotypic diversity in stress adaptation is underpinned by transcriptional and post-transcriptional regulatory molecular mechanisms that could be harnessed to breed for crop resilience [20]. The stress regulatory molecular network in durum wheat is not well understood
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