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Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq]

ABSTRACT: Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE214737 | GEO | 2023/02/15

REPOSITORIES: GEO

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Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]

Project description:Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.

2023-02-15 | GSE214738 | GEO

Transcriptomic in grain and leaf tissues of a low-gluten RNAi wheat line.

Project description:Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reductions of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are independently regulated to the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling.

2022-07-26 | GSE199525 | GEO

Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat

Project description:Common wheat (T. aestivum) converged three subgenomes adapted to different environments. The combinatorial interaction between transcription factors (TFs) and regulatory elements (REs) defines a regulatory circuit that underlies subgenome convergence and divergence. Compared to the relatively conserved gene composition across subgenomes, the intergenic regions with abundant REs is drastically diversified by almost complete TE turnovers, raising major questions regarding how subgenome convergent and divergent regulation is encoded in the highly diversified intergenic regions, and the impact of TE evolution on regulatory conservation and innovation. In the present study, we created genome-wide TF binding catalog to assemble an extensive wheat regulatory network comprising connections among 182 TFs. The different effects of ancient and recent TE insertions on regulatory specificity were observed. Subgenome asymmetric TE expansion is an important source of subgenome divergent TFBS, which help explain the vast occupancy difference across subgenomes. Interestingly, the ancient expansion of RLC_famc1.4-derived TFBS occurred in more than 25% triads promoters. A significant fraction of these TE-derived TFBS subjected to region-specific evolutionary selections, resulting in subgenome-balanced TF binding but unbalanced degeneration of flanking TE sequences. These TE-derived subgenome convergent and divergent regulation linked to subgenome conserved and diversified pathways, suggesting that TEs are an important regulatory driving force contributed to polyploid evolution. Overall, this study demonstrated the impact of TEs on shaping the plasticity and adaptation of common wheat, enriched the theories of TE-promoted transcriptional innovation from the evolutionary aspects of polyploid regulation since first reported by McClintock.

2022-10-08 | GSE192815 | GEO

Spermidine promote the sucrose content in inferior grain and by this improve the grain filling in inferior grain of wheat

Project description:Exogenous spermidine promotes starch sugar metabolism in wheat grains, thereby promoting grain filling

2019-08-14 | GSE135536 | GEO

RNA-seq of developing starchy endosperm of Triticum aestivum at five stages during grain fill

Project description:Transcriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.

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LHP1-mediated conditional repression of subgenome-diversified defenses is responsible for the high plasticity of allopolyploid wheat

Project description:High plasticity of common wheat is attributed to the captured and polyploidization-promoted diversity. However, uncontrolled subgenome diversification can lead to hybrid conflict and dysgenesis, resulting in decreased diversity. How genomic diversity is maintained and interpreted to increase plasticity is unclear. By data-mining from the binding of 193 genome-wide trans-factors and genetic perturbations in common wheat, we identified LHP1 as a major regulator of subgenome-diversified defense genes, enhancer RNAs, and metabolite synthesis-related gene clusters via H3K27me3. Stripe rust infection leads to a global decrease in LHP1-mediated H3K27me3, deprivation of which enhances common wheat stripe rust resistance. We also revealed the consistency between subgenome diversity and population diversity, potentially promoted by LHP1, implying the recent diversification preferentially occurred in the captured subgenome-diversified regions regulated by LHP1. Thus, common wheat benefitted from multi-faced role of LHP1 in promoting sequence diversity and repressing subgenome-diversified defenses; this constraint is eliminated by pathogen infections, enabling timely release and fixation of favorable variations, conferring the evolutionary advantage and high plasticity of common wheat.

2023-10-12 | GSE218538 | GEO

Wheat leaf phosphoproteome under drought stress

Project description:Waxy starch has an important influence on the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and grain yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Our results revealed the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.

2017-01-17 | PXD000646 | Pride

Biostimulant impacts of Glutacetine® and derivated formulations on bread wheat grain proteome

Project description:Nitrogen (N) fertilization is essential in order to insure wheat bread yield and quality. Improving nitrogen use efficiency is therefore crucial for wheat grain protein quality. In the present work, we analysed the effects of new biostimulants containing Glutacetine® or derivate formulations that have been mixed with urea-ammonium-nitrate fertilizer (UAN) on winter wheat grain proteome. A largescale quantitative proteomics analysis of 2 wheat flour fractions led to a dataset of 4369 identified proteins. Quantitative analysis revealed 9, 39 and 96 proteins with a significantly varying abundance after Glutacetine®, VNT1 and VNT4 treatment, respectively, with 11 proteins (or homologue) which were affected by 2 different biostimulants. Major effects affected proteins involved in regulation processes with transcription regulator proteins, in stress responses with biotic and abiotic stress defence proteins, in flowering efficiency with proteins involved in pollen development, in storage functions with the gluten protein alpha-gliadins and starch synthase and in seed development with proteins implied in transport, proteases activity, energy machinery and N pathway. Altogether, our controlled conditions study showed that Glutacetine®, VNT1 and VNT4 biostimulants positively affected protein composition for grain quality.

2021-05-21 | PXD021513 | Pride

Initiation of B-type starch granules in wheat endosperm requires the plastidial α-glucan phosphorylase PHS1.

Project description:PHS1 is a plastidial α-glucan phosphorylase that can elongate and degrade maltooligosaccharides (MOS), but its exact physiological role in plants is poorly understood. Here, we discover a specialised role of PHS1 in establishing the unique bimodal characteristic of starch granules in the wheat endosperm. Wheat endosperm contains large A-type granules that initiate at early grain development, and small B-type granules that initiate in later grain development. We demonstrate that PHS1 interacts with BGC1 – a carbohydrate-binding protein essential for normal B-type granule initiation. Mutants of tetraploid durum wheat deficient in all homeologs of PHS1 had normal A-type granules, but fewer and larger B-type granules. Further, using a double mutant defective in both PHS1 and BGC1, we show that PHS1 is exclusively involved in B-type granule initiation. Grain size and starch content were not affected by the mutations. In leaves, the total starch content and number of starch granules per chloroplast were not affected by loss of PHS1, suggesting that its role in granule initiation in wheat is limited to the endosperm. We therefore propose that the initiation of A- and B-type granules occur by distinct biochemical mechanisms, where PHS1 plays an exclusive role in B-type granule initiation.

2024-01-22 | PXD042396 | Pride

New Insights into the Biosynthesis and Regulation of Wheat Amylose and Amylopectin from Proteomic and Phosphoproteomic Characterization of Granule-binding Proteins

Project description:Waxy starch has an important influence on bread dough and the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. The waxy and non-waxy wheats had similar starch granule morphological features and developmental patterns, and similar amylopectin quality in the grain. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Dynamic transcriptional expression profiling of starch biosynthesis-related genes indicated similar transcriptional expression profiles in both cultivars. Our results revealed that phosphorylation modifications played critical roles in amylose and amylopectin biosynthesis, but the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.

2017-10-30 | PXD002805 | Pride

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