Project description:Tetraploid emmer Triticum turgidum subsp. dicoccum is one of the first wheat species to be domesticated. Emmer shares many pathogen species with modern durum wheat (Triticum turgidum subsp. durum) and hexaploid bread wheat (Triticum aestivum L.). Domesticated emmer is considered a highly valuable source of potentially novel disease resistance genes that can be introduced into modern wheat varieties, however, large gaps remain in our understanding of the basic immune responses of emmer to the most common wheat pathogens. In this work we describe the transcriptional response of emmer to single and mixed pathogen species infections with the ascomycete Zymoseptoria tritici, and the basidiomycete Puccinia graminis. In doing so, we here uncover unique patterns in the response of emmer to a more complex pathogen population with mixed species infections.
Project description:Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. It originates from BBAA wild tetraploid domesticated in Neolithic era, later evolving to domesticated emmer and then to up to 11 T. turgidum subspecies, including durum wheat landraces and modern cultivars. Tetraploid wheat is the donor of the A and B genomes of hexaploid bread wheat (DDAABB), representing therefore a valuable source of genetic variability and beneficial alleles for both durum and bread wheat breeding. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. The expression of 68,154 high confidence genes together with more than 100,000 low confidence, TE-related or long non-coding genes was investigated on 30 diverse tissues from grain, root, leaf, and spike samples across multiple developmental time points to create a transcriptional atlas of durum wheat development.
Project description:Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar, coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. The gene expression was investigated in root and shoot samples collected from plants grown under control condition or subjected to heat, salinity and osmotic stresses or to nitrogen application to create a transcriptional atlas of durum wheat response to abiotic stresses.
Project description:Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar, coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. Gene expression was investigated in spikelets inoculated with Fusarium graminearum and in not infected controls to profile the transcriptional regulation of Fusarium head blight infection.
Project description:Wheat is one of the most significant crops in terms of human consumption in the world. In a climate change scenario, extreme weather event such as heatwaves will be more frequent especially during the grain-filling (GF) stage and could affect grain weight and quality of crops. Molecular mechanisms underlying the response to short heat stress (HS) have been widely reported for the hexaploid wheat (Triticum aestivum) but the regulatory heat stress mechanisms in tetraploid durum wheat (Triticum turgidum ssp. durum) remain partially understood. In this work, we performed a transcriptomic analysis of durum wheat grains to HS during early GF to identify key HS response genes and their predicted regulatory networks under glasshouse conditions.
Project description:Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of durum variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. Overall, we provide a valuable resource for studying endosperm development in this increasingly important crop species.
Project description:The increasing presence of nanoplastics in agricultural soils, particularly polystyrene nanoplastics (PSNPs), poses a novel and underestimated threat to crop productivity and food security. The impact of plastics has recently been investigated in cereals confirming that PSNPs can be absorbed by plants through the roots and subsequently translocated to other plant organs. While extensive research has focused on bread wheat, the effects of PSNPs on durum wheat (Triticum turgidum ssp. durum) remain largely unexplored. In this study, we examined the transcriptomic response to PSNPs exposure in two durum wheat lines: Kronos (wild type) and MRP3, a low-phytate mutant generated via TILLING. The MRP3 line carries deleterious mutation in the Multidrug Resistance-Associated Protein 3 (MRP3) genes, which encodes a vacuolar transporter of phytic acid.
Project description:Gene expression levels of newly synthetic triploid wheat (ABD), its chromosome-doubled hexaploid (AABBDD), stable synthetic hexaploid (AABBDD), and their parents, Triticum turgidum (accession KU124, AABB) and Aegilops tauschii (accession KU2074, DD) were compared to understand genome-wide change of gene expressions during the course of amphidiploidization and genome stabilization. Stable synthetic hexaploid which were maintained through self-pollinations for 13 generations using the same combinations of the parents for production of synthetic common wheat.
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype.