A comprehensive analytical method ‘Regulatome’ revealed a novel pathway for aerenchyma formation under waterlogging in wheat

Physiologia Plantarum, Journal Year: 2025, Volume and Issue: 177(2)

Published: March 1, 2025

Waterlogging is a major abiotic stress restricting crop yield globally, and aerenchyma formation one of the most important adaptive strategies in waterlogging-tolerant plants. However, conservation this process remains poorly understood, additional pathways are yet to be identified. Here, physiological, anatomical, transcriptomic, metabolomic analyses were conducted on wheat seedlings under normal waterlogging conditions. caused growth inhibition physiological damage, as well induced roots. A total 10,346 differentially expressed genes 3,419 differential metabolites identified In addition AP2/ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) gene family, integrating also revealed role LOB/AS2 (LATERAL ORGAN BOUNDARIES/ASYMMETRIC LEAVES2) waterlogging. It was that classical pathway mediated by ethylene response, synergy calcium ion reactive oxygen species, deeply conserved both monocots eudicots during 160 million years evolution through co-expression networks cross-species. The newly introduced concept 'Regulatome' supported formation, with proposed model jasmonic acid signalling involved waterlogging, suggesting its usefulness identification function exploration. These findings provide novel insight into regulatory mechanisms breeding approaches for developing cultivars high tolerance.

Language: Английский

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Genome-wide identification and expression analysis of bHLH gene family revealed their potential roles in abiotic stress response, anthocyanin biosynthesis and trichome formation in Glycyrrhiza uralensis

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

Published: Jan. 21, 2025

Introduction Licorice stands out as an exceptional medicinal resource with a long history of application, attributed to its substantial pharmacological potential. The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family, being the second-largest in plants, is vital for plant development and adapting environmental shifts. Despite this, comprehensive characteristics licorice bHLH family are not well-documented. Results In this study, detailed thorough genome-wide identification expression analysis Glycyrrhiza uralensis was carried out, resulting 139 members. Our duplication highlighted significant contribution segmental duplications expansion G. genes, GubHLH genes experiencing negative selection throughout evolution. It discovered that GubHLH64 GubHLH38 could be importantly linked trichome initiation anthocyanin biosynthesis also involved abiotic stress response. Additionally, certain subfamily III (d+e) members implicated drought GubHLH108, GubHLH109, GubHLH116 were suggested form tightly related cluster, initiating transcriptional responses via JA signaling pathway. Discussion summary, our findings furnish foundational understanding future investigations functions regulation mechanisms, shedding light on potential applications medicine agriculture.

Language: Английский

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Identification of stay-green candidate gene TaTRNH1-3B and development of molecular markers related to chlorophyll content and yield in wheat (Triticum aestivum L.)

Plant Physiology and Biochemistry, Journal Year: 2025, Volume and Issue: 222, P. 109787 - 109787

Published: March 14, 2025

Language: Английский

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Cloning and Functional Study of AmGDSL1 in Agropyron mongolicum

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9467 - 9467

Published: Aug. 30, 2024

Agropyron mongolicum Keng is a diploid perennial grass of triticeae in gramineae. It has strong drought resistance and developed roots that can effectively fix the soil prevent erosion. GDSL lipase or esterases/lipase variety functions, mainly focusing on plant abiotic stress response. In this study, gene from A. mongolicum, designated as AmGDSL1, was successfully cloned isolated. The subcellular localization AmGDSL1 (pCAMBIA1302-AmGDSL1-EGFP) results showed protein only localized cytoplasm. When transferred into tobacco (Nicotiana benthamiana), heterologous expression led to enhanced tolerance. Under stress, overexpressing plants fewer wilting leaves, longer roots, larger root surface area. These overexpression lines possessed higher superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), proline (PRO) activities. At same time, malondialdehyde (MDA) content lower than wild-type (WT) tobacco. findings shed light molecular mechanisms involved gene’s role resistance, contributing discovery utilization drought-resistant genes for enhancing crop resistance.

Language: Английский

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Regulation of tillering and panicle branching in rice and wheat

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

Published: Dec. 1, 2024

Language: Английский

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Integrative Omics reveals genetic basis and TaMYB7-A1’s function in wheat WUE and drought resilience

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

Published: Dec. 23, 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

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CSGDN: contrastive signed graph diffusion network for predicting crop gene–phenotype associations

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

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Influences of residual stomatal conductance on the intrinsic water use efficiency of two C3 and two C4 species

Agricultural Water Management, Journal Year: 2024, Volume and Issue: 306, P. 109136 - 109136

Published: Nov. 20, 2024

Language: Английский

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Genome-wide identification and expression analysis of CASPL gene family in Zea mays (L.)

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

Published: Oct. 28, 2024

Casparian strip membrane domain proteins like (CASPL), exhibit profound associations with root development, stress responsiveness and mineral element uptake in plants. Nonetheless, a comprehensive bioinformatics analysis of the ZmCASPL gene family maize remains unreported. In study, we have identified 47 members at whole-genome level, systematically classifying them into six distinct groups. Furthermore, our revealed that same group contains similar structures conserved motifs. Duplication events showed whole genome duplication (WGD) tandem (TD) contribute to generation together maize, but former plays more prominent role. observed most genes contain MYB-binding sites (CAACCA), which are associated strip. Utilizing RNA-seq data, found ZmCASPL21 ZmCASPL47 specifically highly expressed only roots. This finding implies may be involved development. Additionally, illuminated drought, salt, heat, cold stresses, low nitrogen phosphorus conditions, as well pathogen infection, significantly impact expression patterns genes. RT-qPCR 5/13/25/44 different under PEG NaCl treatments. Collectively, these findings provide robust theoretical foundation for further investigations functional roles maize.

Language: Английский

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The Wheat Hsf Transcription Factor Tahsfc3b Confers Drought Tolerance Through ROS Scavenging and Aba Pathway in Transgenic Arabidopsis and Wheat

Published: Jan. 1, 2024

Language: Английский

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