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

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 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.

Язык: Английский

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

Zhaoheng Zhang,

Xuelei Lin

и другие.

Science Advances, Год журнала: 2025, Номер 11(22)

Опубликована: Май 30, 2025

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 fine-scale chromatin interactions four major crops: rice, sorghum, maize, wheat. TAC-C reveals strong association between interaction frequency expression, particularly emphasizing the conserved roles of hub anchors genes across crop species. Integrating structure with population genetics data highlights that loops connect distal regulatory phenotypic variation. In addition, asymmetrical open among subgenomes, driven by transposon insertions sequence variations, contribute biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related through interactions, enhanced photosynthetic efficiency starch content Taspl7&15 mutant. provides insights into crops, especially SPL-mediated photosynthesis regulation

Язык: Английский

Процитировано

0
Integrative Omics reveals genetic basis and TaMYB7-A1’s function in wheat WUE and drought resilience DOI Creative Commons
Jun Xiao, Yuxin Zhou, Hao Wang

и другие.

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Дек. 23, 2024

Abstract Improving water use efficiency (WUE) and drought resistance in wheat is critical for ensuring global food security under changing climate conditions. Here, we integrated multi-omic data, including population-scale phenotyping, transcriptomics, genomics, to dissect the genetic molecular mechanisms underlying WUE resilience wheat. Genome-wide association studies (GWAS) revealed 8,135 SNPs associated with WUE-related traits, identifying 258 conditional non-conditional QTLs, many of which co-localized known drought-resistance genes. Pan-transcriptome analysis uncovered tissue-specific expression patterns, core unique gene functions, dynamic sub-genomic biases response drought. eQTL mapping pinpointed 146,966 regulatory loci, condition-specific hotspots enriched genes involved regulation, osmoregulation, photosynthesis. Integration Weighted co-expression network (WGCNA), Summary-data-based Mendelian Randomization (SMR) GWAS, eQTLs identified 207 candidate causal as key regulators traits wheat, such TaMYB7-A1. Functional analyses found that TaMYB7-A1 enhances tolerance by promoting root growth, reducing oxidative stress, improving osmotic enabling better access survival stress. It also increases photosynthesis WUE, boosting yield without compromising performance well-watered conditions, making it ideal target breeding. Our findings provide a comprehensive omic framework understanding architecture resistance, offering valuable targets breeding resilient varieties.

Язык: Английский

Процитировано

1
TaDL interacts with TaB3 and TaNF‐YB1 to synergistically regulate the starch synthesis and grain quality in bread wheat DOI Creative Commons

Guoyu Liu,

Runqi Zhang, Zhenlong Wu

и другие.

Journal of Integrative Plant Biology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 23, 2024

ABSTRACT Starch biosynthesis is a critical factor in wheat ( Triticum aestivum L.) quality and yield. However, the full scope of its regulation not fully understood. Here we report that TaDL interacts with TaB3 TaNF‐YB1 to synergistically regulate starch wheat. Genome‐edited tadl mutant lines had smaller lighter grains lower total amylose contents compared wild type (WT). Correspondingly, transcript levels biosynthesis‐related genes, including TaSUS1 , TaSUS2 TaAGPL2 TaSBEIIa TaGBSSII TaSWEET2a were markedly at 15 d after flowering (DAF) mutants. physically interacted activated transcription through direct binding their promoter regions. A null also affected grain filling, phenotypes similar those mutants, whereas overexpression promoted filling. Our study demonstrated plays an essential role identified elite allele TaDL‐BI ) associated content, providing insights into underlying molecular mechanism which may be useful breeding high‐yielding improvement.

Язык: Английский

Процитировано

1
Integrated Transcriptomic and Proteomic Analyses Revealed Molecular Mechanism Underlying Nutritional Changes During Seed Development of Chenopodium Quinoa DOI
Nazer Manzoor,

Jiahong Yuan,

Wenhua Dongcheng

и другие.

Опубликована: Янв. 1, 2024

Язык: Английский

Процитировано

0
Integrative Omics reveals genetic basis and TaMYB7-A1's function in wheat WUE and drought resilience DOI Creative Commons
Jun Xiao, Yuxin Zhou, H. M. Wang

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 13, 2024

Improving water use efficiency (WUE) and drought resistance in wheat is critical for ensuring global food security under changing climate conditions. Here, we integrated multi-omic data, including population-scale phenotyping, transcriptomics, genomics, to dissect the genetic molecular mechanisms underlying WUE resilience wheat. Genome-wide association studies (GWAS) revealed 8,135 SNPs associated with WUE-related traits, identifying 258 conditional non-conditional QTLs, many of which co-localized known drought-resistance genes. Pan-transcriptome analysis uncovered tissue-specific expression patterns, core unique gene functions, dynamic sub-genomic biases response drought. eQTL mapping pinpointed 146,966 regulatory loci, condition-specific hotspots enriched genes involved regulation, osmoregulation, photosynthesis. Integration Weighted co-expression network (WGCNA), Summary-data-based Mendelian Randomization (SMR) GWAS, eQTLs identified 207 candidate causal as key regulators traits wheat, such TaMYB7-A1. Functional analyses found that TaMYB7-A1 enhances tolerance by promoting root growth, reducing oxidative stress, improving osmotic enabling better access survival stress. It also increases photosynthesis WUE, boosting yield without compromising performance well-watered conditions, making it ideal target breeding. Our findings provide a comprehensive omic framework understanding architecture resistance, offering valuable targets breeding resilient varieties.

Язык: Английский

Процитировано

0
Reshaping epigenomic landscapes in facilitating the speciation of bread wheat DOI Creative Commons
Zhaoheng Zhang, Xuelei Lin, Jingjing Yue

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 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.

Язык: Английский

Процитировано

0