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

Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat DOI
Xuemei Liu, Min Deng,

Bingxin Shi

et al.

Science China Life Sciences, Journal Year: 2024, Volume and Issue: 67(10), P. 2251 - 2266

Published: July 8, 2024

Language: Английский

Citations

2
Regulation of tillering and panicle branching in rice and wheat DOI Creative Commons
Ning Zhang, Yuhao Liu, Songtao Gui

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

Citations

1
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

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 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.

Language: Английский

Citations

1
CSGDN: contrastive signed graph diffusion network for predicting crop gene–phenotype associations DOI Creative Commons

Yiru Pan,

Xingyu Ji,

Jin Jong You

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract Positive and negative association prediction between gene phenotype helps to illustrate the underlying mechanism of complex traits in organisms. The transcription regulation activity specific genes will be adjusted accordingly different cell types, developmental timepoints, physiological states. There are following two problems obtaining positive/negative associations phenotype: (1) high-throughput DNA/RNA sequencing phenotyping expensive time-consuming due need process large sample sizes; (2) experiments introduce both random systematic errors, and, meanwhile, calculations or predictions using software models may produce noise. To address these issues, we propose a Contrastive Signed Graph Diffusion Network, CSGDN, learn robust node representations with fewer training samples achieve higher link accuracy. CSGDN uses signed graph diffusion method uncover regulatory phenotypes. Then, stochastic perturbation strategies used create views for original diffusive graphs. Lastly, multiview contrastive learning paradigm loss is designed unify presentations learned from resist interference reduce We perform validate performance three crop datasets: Gossypium hirsutum, Brassica napus, Triticum turgidum. results show that proposed model outperforms state-of-the-art methods by up 9. 28% AUC sign G. hirsutum dataset. source code our available at https://github.com/Erican-Ji/CSGDN.

Language: Английский

Citations

1
Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii DOI Creative Commons

Zhiwen Zhai,

Yuqing Che,

Shuaifeng Geng

et al.

Plants, Journal Year: 2024, Volume and Issue: 13(9), P. 1259 - 1259

Published: April 30, 2024

JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development environmental adaptation. Despite wheat being one of main staple food crops, until recently, comprehensive analysis its

Language: Английский

Citations

1
Genetic improvement of important agronomic traits in Chinese wheat breeding over the past 70 years DOI Creative Commons

Lei Zhuang,

Haixia Liu, Jian Hou

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Nov. 29, 2024

Understanding the genetic improvement patterns of agronomic traits in Chinese wheat (Triticum aestivum L.) breeding is essential for devising future strategies. However, a systematic analysis important lacking. This study aimed to provide insights into progress yield-related process and clarify selection pressure on different agroecological zones. Phenotypic evaluations 481 accessions including 157 landraces (CLs) 324 modern cultivars (MCCs), were carried out multiple locations years. The population structure analyses showed that all could be basically divided CLs MCCs subpopulations. Pearson correlation revealed negative between grain number per spike thousand-grain weight gradually decreased while weight, spike, effective tiller exhibited synergistic improvements during process. differences among released from 1950s 2000s indicated weight-related increased linearly, whereas plant height significantly. Furthermore, since 1950s, heading date, flowering maturity date have become earlier, length spikelet not changed significantly with advancement annual gain had greatest increase (‒0.96%), followed by (0.38%), lowest (0.13%). difference geographical origins further height, width, thickness experienced strong same trend seven Among zones, northern winter zone strongest pressure, strongly selected reveals China obvious phenotypic differences, breeding, will inevitably involve continuous spike.

Language: Английский

Citations

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

et al.

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

Published: Dec. 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.

Language: Английский

Citations

0
Integrated Transcriptomic and Proteomic Analyses Revealed Molecular Mechanism Underlying Nutritional Changes During Seed Development of Chenopodium Quinoa DOI
Nazer Manzoor,

Jiahong Yuan,

Wenhua Dongcheng

et al.

Published: Jan. 1, 2024

Language: Английский

Citations

0
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

Citations

0