Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Advanced Science, Год журнала: 2024, Номер 11(33)

Опубликована: Июнь 28, 2024

Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, H3K27me3 collectively regulate SSP starch genes with varying impact. Population transcriptome phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing quality in core collection of accessions. Integration time-serial RNA-seq ATAC-seq enables the construction hierarchical transcriptional network identifying 42 high-confidence novel candidates. These candidates exhibit overlap regions associated size traits, functional significance validated through expression-phenotype association analysis among accessions loss-of-function mutants. Functional abscisic acid insensitive 3-A1 (TaABI3-A1) genome editing knock-out lines demonstrates its promoting accumulation while repressing biosynthesis regulation. Excellent TaABI3-A1

Язык: Английский

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Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Ноя. 6, 2024

Dissecting the genetic basis of seed traits in wheat is impeded by limited polymorphisms and significant variations caused environmental conditions position a spikelet. Seed performance largely determined endosperm development controlled spatiotemporal variation gene activities, which greatly affected chromatin status. Here, we map genome-wide dynamic distributions H3K27me3, H3K4me3 H3K9ac modifications profile transcription across development. The combinatorial effects active repressive marks ensure expression, especially for starch biosynthesis. By scanning factor binding motifs ATAC-seq peaks, hub regulators are identified from regulatory network. In addition, observe correlations between sequence germplasm population. Thus, analysis genomic activities together with provides robust approach to dissect bread wheat. Dynamic changes histone modification how it affects during remain unknow. author fulfill this knowledge gap reveal role ethylene response ERF5 network grain filling, protein accumulation.

Язык: Английский

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TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 10, 2025

Abstract Cis -regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce Transposase-Accessible Chromosome Conformation Capture (TAC-C), a method integrating ATAC-seq Hi-C to capture fine-scale chromatin interactions four major crops: rice, sorghum, maize, wheat. TAC-C reveals that interaction frequency aligns with genome size expression, exhibiting distinct loop structures between C3 C4 plants, particularly C4-specific enzymes coding genes. Integrating structure population genetics data highlights loops connect distal regulatory phenotypic variation. Asymmetrical open among subgenomes, driven by transposon insertions sequence variations, contribute biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through interactions, enhanced photosynthetic efficiency starch content Taspl7&15 mutant. provides new insights into the of crops, especially SPL-mediated photosynthesis regulation Teaser Reveals Chromatin Interactions SPL-Mediated Photosynthesis Regulation Crops.

Язык: Английский

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Genome-wide analysis of Q binding reveals a regulatory network that coordinates wheat grain yield and grain protein content

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Wheat is an important cereal crop used to produce diverse and popular food worldwide because of its high grain yield (GY) protein content (GPC). However, GY GPC are usually negatively correlated. We previously reported that favorable alleles the wheat domestication gene Q can synchronously increase GPC, but underlying mechanisms remain largely unknown. In this study, we investigated regulatory network involving associated with in young grains through DNA affinity purification sequencing transcriptome analyses, electrophoretic mobility shift dual-luciferase assays, transgenic approaches. Three Q-binding motifs, namely TTAAGG, AAACA[A/T]A, GTAC[T/G]A, were identified. Notably, genes related photosynthesis or carbon nitrogen metabolism enriched regulated by Q. Moreover, was revealed bind directly own glutamine synthetase TaGSr-4D expression, thereby influencing assimilation during filling stage increasing GPC. Considered together, our study findings provide molecular evidence positive effects on

Язык: Английский

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ISDH‐seq: a robust methodology for profiling and characterization of open chromatin

Plant Biotechnology Journal, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Profiling of open chromatin is essential for understanding regulatory mechanisms that govern DNA-templated events. However, methodology-dependent detection sites (OCSs) has been reported in both humans and plants. Therefore, there a pressing need any reliable orthogonal methodologies to broaden the identification across genome, particularly We here report development an situ DNase I hypersensitivity sequencing (ISDH-seq) efficient characterization chromatin, which can be applicable 50-200 K nuclei. This technique identifies 72% 120% more OCSs than newly generated DNase- ATAC-seq from same batch tissues as ISDH, respectively, rice genome. As compared DH-specific OCSs, ISDH-specific exhibit distinct epigenetic features, including relative hypomethylation, higher frequency associated with H3K27me3 increased associations spatial interactions. Genes H3K27me3-enriched tend expressed stress- tissue-dependent manner, have significant biological implications. The functions may mediated by TF-centred networks or through loops. Importantly, subset genes co-regulated distal (dOCSs) loops are evolutionarily conserved regulated single trans-OCS, domesticated responsible important agronomic traits. Thus, ISDH-seq enrich expand landscapes, facilitating better their implications plant genomes. It could serve method complements existing techniques adapted use non-plant systems.

Язык: Английский

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Time‐course transcriptome and chromatin accessibility analyses reveal the dynamic transcriptional regulation shaping spikelet hull size

The Plant Journal, Год журнала: 2025, Номер 122(1)

Опубликована: Апрель 1, 2025

SUMMARY The grains of rice ( Oryza sativa ) are enclosed by a spikelet hull comprising the lemma and palea. Development determines storage capacity grain, thus affecting grain yield quality. Although multiple signaling pathways controlling size have been identified, transcriptional regulatory mechanisms underlying development remain limited. Here, we used RNA‐seq ATAC‐seq to characterize transcription chromatin accessibility dynamics during hulls. A time‐course analysis showed that more than half genes were sequentially expressed most open regions (OCRs) changed moderately, although some positively or negatively affected expression their closest genes. We revealed crucial role GROWTH‐REGULATING FACTORs in shaping influencing metabolic pathways, coordinated regulation response auxin cytokinin signaling. also demonstrated function SCL6‐IIb, member GRAS family factors, regulating size, with SCL6‐IIb being activated SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE 18 (OsSPL18). When edited DNA sequences within OCRs upstream start codon BRASSINAZOLE‐RESISTANT 1 BZR1 , generated mutant lines longer grains. These findings offer comprehensive overview cis ‐regulatory landscape involved forming valuable resource for exploring network behind development.

Язык: Английский

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Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat

Genome biology, Год журнала: 2025, Номер 26(1)

Опубликована: Апрель 11, 2025

Cereal grain size and quality are critical agronomic traits in crop production. Wheat development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene expression to establish functional compartments different cell types. Here, we perform a spatial transcriptomics study covering the early stages wheat development, from 4 12 days after pollination. We classify into 10 distinct types identify 192 marker genes associated with them. WGCNA analysis reveals highly expressed exhibit enrichment patterns, significantly influencing filling. Through co-expression motif analyses, specific group may regulate including TaABI3-B1, transcription factor specifically embryo surrounding endosperm, which negatively affects size. This presents comprehensive transcriptional dataset for understanding development. Additionally, it identifies key genetic resources potential applications improving yield.

Язык: Английский

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Uncovering the transcriptional regulatory network underlying Selenium tolerance in maize seedlings

Journal of Hazardous Materials, Год журнала: 2025, Номер 494, С. 138437 - 138437

Опубликована: Апрель 28, 2025

Язык: Английский

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Epigenetic perspectives on wheat speciation, adaptation, and development

Trends in Genetics, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

Язык: Английский

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Genetic effect of the Ph1 locus on transcriptome atlas of anther development‐related genes, meiotic chromosome behavior and agronomic traits in bread wheat

The Plant Journal, Год журнала: 2025, Номер 122(3)

Опубликована: Май 1, 2025

SUMMARY Proper spatiotemporal expression of meiosis‐related genes (MRGs) and other male‐microsporogenesis/microgametogenesis‐related (MMRGs) is crucial for normal anther development, yet their patterns remain largely unknown in wheat. The Ph1 locus wheat known to contain the gene that plays a dual role promoting pairing between homologous chromosomes but repressing homoeologous chromosomes, its genetic function still unclear. Here, we investigated these issues by conducting comprehensive transcriptome analysis during development Chinese Spring (CS) ph1b deletion mutant under greenhouse field conditions. Our results revealed MRGs MMRGs are predominantly expressed pre‐meiosis stages, with also being highly meiotic‐II. Gene co‐expression showed C2H2 B3 transcriptional factors (TFs) associated MRGs, MYB regulators interacted mainly microgametogenesis. Deletion within failed induce compensatory activation counterparts, while outside environmental‐specific responses, especially meiotic‐II mature pollen stages. Notably, early disjunction bivalent primary factor leading defective meiocytes metaphase I. Furthermore, exhibited substantially delayed heading date, potentially contributing environment‐stable environment‐specific alterations fertility grain‐related traits. study highlights significant impact on previously unheeded effect meiotic chromosome agronomic traits, suggesting potential manipulations improvement.

Язык: Английский

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