Sporolithon durum
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ABSTRACT:
PROVIDER: PRJNA318306 | ENA |
REPOSITORIES: ENA
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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.
2026-07-29 | GSE318160 | GEO
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.
2026-07-29 | GSE318338 | GEO
Project description:Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. Yield loss in durum wheat can be exacerbated due to minimal rainfall in the early reproductive stages of development during Spring in Australia. This study describes genotypic differences in the miRNAome between water deficit tolerant/sensitive durum, using flag leaf and developing head tissue, and more specifically identifies miRNAs associated with water deficit stress. Results: Small RNA libraries (96 in total) were constructed from flag leaf and developing head tissues of four durum genotypes (Tamaroi, Yawa, EGA Bellaroi, Tjilkuri), with or without water deficit stress. Illumina sequencing and subsequent analysis detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins. Statistical analysis of the abundance of sequencing reads revealed 66 conserved miRNAs and five novel miRNA hairpins showing differential expression under water deficit stress. During stress, several conserved and novel miRNAs showed unambiguous inverted regulatory profiles between the durum genotypes studied. Several miRNAs were also identified to have different abundance in the flag leaf compared to the developing head regardless of treatment. Predicted mRNA targets from four novel durum miRNAs were characterised using Gene Ontology (GO) which revealed functions common to stress responses and plant development. Conclusion: For the first time, we present a comprehensive study of the miRNA transcriptome of flag leaf and developing head tissues in different durum genotypes under water deficit stress. The identification of differentially expressed miRNAs provides molecular evidence that miRNAs are potential determinants of water stress tolerance in durum wheat. GO analysis of predicted targets contributes to the understanding of genotype-specific physiological responses leading to stress tolerance capacity. Further functional analysis of specific stress responsive miRNAs identified, and their interaction with mRNA targets is ongoing and will assist in developing future durum wheat varieties with enhanced water deficit stress tolerance.
2015-10-01 | GSE69339 | GEO
Project description:Durum wheat is an important cereal crop grown mainly in semi-arid environments (e.g. Mediterranean regions) characterized by water scarcity and high temperatures often occurring at the same time. This work reports on a transcriptomic analysis carried out on two durum wheat cultivars (Cappelli and Ofanto) characterized by different water use efficiency (WUE), grown to booting stage and subjected to a combination of drought and heat stresses, a situation similar to the experience of a crop grown in Mediterranean environments and exposed to a terminal heat/drought stress. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, alessio. The equivalent experiment is TA47 at PLEXdb.]
2016-03-22 | GSE45563 | GEO
Project description:Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in germination time-course and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly has revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provides the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for superior breeding germplasm and/or varieties.
2020-02-04 | GSE143454 | GEO
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.
2026-06-25 | E-MTAB-15975 | biostudies-arrayexpress
Project description:Two durum wheat (Triticum turgidum L. var. durum) genotypes, the variety Borgia (derived from the cross IRTA-1004 x Bidi 17) and a pale-green mutant (MD-597) derived from it, were used for the measurement of physiological traits and gene expression. Mutant plants used for this study were the stable eight generation (M8) derived from the isolated original mutant plant. Terminal water stress: irrigation was drastically reduced from the booting stage until maturity by watering the pots with the amount of water necessary to maintain the pots at 1/3 of field capacity. The drought treatment was started by withholding water at the anthesis stage. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA48 at PLEXdb.]
2016-05-09 | GSE47090 | GEO
Project description:Durum wheat meristem transcriptome
| PRJNA795036 | ENA
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.
2022-10-25 | GSE216253 | GEO