Reshaping epigenomic landscapes in facilitating the speciation of bread wheat DOI Creative Commons
Zhaoheng Zhang, Xuelei Lin, Jingjing Yue

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 27, 2024

Summary Polyploidization is a driving force of wheat evolution and speciation, yet its impact on epigenetic regulation gene expression remains unclear. Here, we constructed high-resolution landscape across leaves, spikes, roots hexaploidy tetraploid diploid relatives. Inter-species stable-expression genes exhibited conserved amino acid sequences under strong purifying selection, while dynamic-expression were linked to species-specific adaptation. During hexaploidization, dominant D-subgenome homoeolog was suppressed via reduced activating signals, converging with the A B subgenomes. Proximal chromatin regions near more stable, whereas distal regions, particularly enhancer-like elements mediated by H3K27ac H3K4me3, exhibit higher dynamism. Sequence variations in these enhancers lead differential regulation, influencing traits such as spike development. For instance, two haplotypes dCRE region TaDEP-B1 resulted significant differences spikelet numbers. We also observed coevolution transcription factors their binding sites, within expanded ERF family, which regulates morphology. This study highlights interplay between sequence variation modifications shaping transcriptional during offering valuable insights for genetic improvement.

Language: Английский

Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement DOI Creative Commons
Long Zhao, Jinchao Chen,

Zhaoheng Zhang

et al.

Advanced Science, Journal Year: 2024, Volume and Issue: 11(33)

Published: June 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

Language: Английский

Citations

12
TabHLH27 orchestrates root growth and drought tolerance to enhance water use efficiency in wheat DOI
Dongzhi Wang, Xiuxiu Zhang, Yuan Cao

et al.

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(7), P. 1295 - 1312

Published: May 2, 2024

ABSTRACT Cultivating high‐yield wheat under limited water resources is crucial for sustainable agriculture in semiarid regions. Amid scarcity, plants activate drought response signaling, yet the delicate balance between tolerance and development remains unclear. Through genome‐wide association studies transcriptome profiling, we identified a atypical basic helix‐loop‐helix (bHLH) transcription factor (TF), TabHLH27‐A1, as promising quantitative trait locus candidate both relative root dry weight spikelet number per spike wheat. TabHLH27‐A1/B1/D1 knock‐out reduced tolerance, yield, use efficiency (WUE). TabHLH27‐A1 exhibited rapid induction with polyethylene glycol (PEG) treatment, gradually declining over days. It activated stress genes such TaCBL8‐B1 TaCPI2‐A1 while inhibiting growth like TaSH15‐B1 TaWRKY70‐B1 short‐term PEG stimulus. The distinct transcriptional regulation of involved diverse interacting factors TaABI3‐D1 TabZIP62‐D1. Natural variations influence its responses to stress, Hap‐II associated stronger larger system, more spikelets, higher WUE Significantly, excellent was selected during breeding process China, introgression allele improved grain especially water‐limited conditions. Our study highlights TabHLH27‐A1's role balancing providing genetic manipulation enhancing

Language: Английский

Citations

10
Recent advances in exploring transcriptional regulatory landscape of crops DOI Creative Commons
Qiang Huo, Rentao Song, Zeyang Ma

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: June 5, 2024

Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of phenotype by altering the expression particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend transcriptional mechanisms that underpin these In multi-omics era, a large amount omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, single-cell omics. The abundant resources emergence advanced computational tools offer unprecedented opportunities obtaining holistic view profound understanding processes linked desirable This review focuses on integrated network approaches utilize investigate gene regulation. Various types networks their inference methods are discussed, focusing recent advancements in plants. integration proven be crucial construction high-confidence networks. With refinement methodologies, they will significantly enhance efforts contribute global food security.

Language: Английский

Citations

4
The Class III Peroxidase gene TaPRX-2A controls grain number per spike in common wheat (Triticum aestivum L.) DOI Creative Commons

Dongtian Zang,

Wenjia You,

Yangyang Wu

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Feb. 6, 2025

Some peroxidases (PRXs) are involved in abiotic stress response. However, to the best of our knowledge, effects PRXs on agronomic traits including grain number per spike (GNS), spikelet (SNS) and length (SL) also largely unknown. In study, we cloned a wheat PRX gene TaPRX-2A identified its function controlling GNS by generating transgenic overexpression lines. The results showed that displayed lower shorter SL, compared with wild-type plants. RNA-seq analysis indicated alterations various pathways flavonoid biosynthesis, lignin phytohormone signaling, as well sucrose starch biosynthesis. Co-expression transcription factors, such bHLH, WRKY, bZIP may be regulation genes associated these pathways. Our findings provide insights into mechanisms which regulate traits, illustrating potential applicability crop improvement programs.

Language: Английский

Citations

0
TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation DOI Creative Commons

Jingmin Kang,

Zhaoheng Zhang,

Xuelei Lin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 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.

Language: Английский

Citations

0
Decoding cellular transcriptional regulatory networks governing wheat inflorescence development DOI Creative Commons
Jun Xiao, Xuemei Liu, Xuelei Lin

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 12, 2025

Abstract In wheat, inflorescence architecture critically determines yield potential, yet its structural complexity and asynchronous development have hindered cellular-resolution studies of spikelet floret formation. Here, we integrate spatial transcriptomics, high-sensitivity multiplexed error-robust fluorescence in situ hybridization (MERFISH), snRNA-seq across six developmental stages to generate a spatiotemporal atlas the wheat inflorescence. We identified 20 cell types, spatially resolved into three categories: 1) proliferating cells within spikelet, marked by active division; 2) supporting along central axis, including pith, cortex, vasculature; 3) developmental located both inside at base spikelets. The multi-omics approach enabled identification rare type ovary. Trajectory inference revealed that spikelets florets originate from two temporally distinct sub-clusters proliferating cells (R7), each defined high expression regulators. These findings challenge conventional model sequential meristem transitions (inflorescence-spikelet-floret) in wheat. Integration time-series snATAC-seq delineated cellular transcriptional regulatory networks (cTRNs) governing formation, mediated auxin cytokinin signaling, driven MADS-box transcription factors. Cell identity was maintained type-specific accessible chromatin regions (csACRs), which are enriched for SNPs associated with spike-related traits. For instance, csACRs WFZP DUO1 promoters affect TaNAC30 binding, regulating supernumerary phenotypes. Our work provides mechanistic framework identifies cTRN nodes as potential targets optimizing yield-related architecture.

Language: Английский

Citations

0
The Q‐interacted protein QIP3 recruits TaTPL to regulate spike architecture in wheat DOI
Ziyi Yang, Wanqing Bai,

Guanghui Guo

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(2)

Published: April 1, 2025

SUMMARY Spike architecture is a critical determinant of grain yield in wheat; yet the regulatory mechanisms remain poorly understood. Here, we demonstrate that AP2 transcription factor Q directly represses expression TaMYB30‐6A , gene associated with spike length wheat. We further identify QIP3 as Q‐interacting protein harboring an N‐terminal EAR motif. Simultaneously, reveal exhibits transcriptional repression activity, dependent on motif, and physically interacts corepressor TaTPL. Importantly, clustered regularly interspaced short palindromic repeats/CRISPR‐associated 9 (CRISPR/Cas9)‐generated qip3‐aabbdd mutants exhibit reduced plant height increased phenotypes. Furthermore, RNA‐seq RT‐qPCR assays show negatively regulates target Collectively, propose motif‐containing to regulate by recruiting TaTPL

Language: Английский

Citations

0
Integrating evolutionary genomics of forest trees to inform future tree breeding amidst rapid climate change DOI Creative Commons
Jiajun Feng, Xuming Dan,

Yangkai Cui

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(10), P. 101044 - 101044

Published: Aug. 7, 2024

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats biodiversity nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems play a crucial role combating mitigating the adverse effects extreme events, despite their own vulnerability these threats. Therefore, understanding monitoring how natural forests respond key priority for conservation. Recent progress evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools address several issues. These include precise delineation species units, inference past histories demographic fluctuations, identification environmentally adaptive variants, measurement genetic load levels. As urgency deal with more stresses grows, genomics history, local adaptation, future responses change, conservation restoration forest will be critical research at nexus global population biology. In this review, we explore application assess using approaches discuss outlook breeding climate-adapted trees.

Language: Английский

Citations

3
qSL2B/TaeEF1A regulates spike development and grain number in wheat DOI Creative Commons
Qiang Yan, Yunlong Pang, Yue Lu

et al.

The Crop Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Epigenetic perspectives on wheat speciation, adaptation, and development DOI
Xuemei Liu, Dongzhi Wang,

Zhaoheng Zhang

et al.

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

Citations

0