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, Год журнала: 2025, Номер 222, С. 109787 - 109787

Опубликована: Март 14, 2025

Язык: Английский

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

Physiologia Plantarum, Год журнала: 2025, Номер 177(2)

Опубликована: Март 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.

Язык: 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, Год журнала: 2024, Номер unknown

Опубликована: Дек. 1, 2024

Язык: 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, Год журнала: 2025, Номер 15

Опубликована: Янв. 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.

Язык: Английский

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Maize leaf yellowing gene ZmCAAX modulates growth and drought resistance by regulating abscisic acid contents through interaction with the ABA biosynthetic enzyme ZmNCED3

Plant Biotechnology Journal, Год журнала: 2025, Номер unknown

Опубликована: Июнь 3, 2025

Summary In maize ( Zea mays L.), leaves are essential for photosynthesis and transpiration leaf yellowing is regulated by carotenoid metabolism, hormonal signalling environmental factors. However, the molecular mechanisms linking drought stress remain poorly understood. ZmNCED3, a key regulator of degradation responses, plays critical role in ABA biosynthesis, but its upstream regulatory unclear. This study investigates association between leaf‐yellowing mutations response maize. Through map‐based cloning allelism tests, we identified ZmCAAX as causal gene underlying yp1 mutant phenotype. encodes CAAX amino‐terminal protease family protein. Overexpression increases sensitivity, whereas knockout mutants exhibit enhanced resistance. physically interacts with ZmNCED3 promotes degradation. Under stress, expression decreases, resulting increased levels, which turn biosynthesis. Based on these findings, designing knockouts or selecting natural variant alleles could significantly enhance resistance content. genetic strategy may be applied to breeding improve quality

Язык: Английский

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Full-length transcriptome provides insights into the molecular regulation of seed spike number in Agropyron mongolicum

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Июнь 3, 2025

Agropyron mongolicum is a xerophytic perennial grass with good palatability and nutritional value, predominantly distributed in sandy, arid regions desert steppes of northwest China. However, its low biomass limited seed yield pose significant challenges for large-scale cultivation forage production. To date, there have been genomic or transcriptomic studies on A. , particularly regarding the molecular genetic mechanisms underlying yield-related traits. In this study, we employed an integrated approach combining long-read sequencing (PacBio Iso-Seq) short-read (Illumina RNA-seq) to generate comprehensive full-length transcriptome from four tissues—leaves, stems, young spikes, mature spikes. Transcriptomic comparisons between multi-spike few-spike germplasms were performed identify candidate genes involved regulation spike number. A total 762,116 transcripts generated, among which 214,500 successfully annotated. We identified 185,424 unique genes, including 91,514 differentially expressed (DEGs). Functional enrichment analysis revealed 43 DEGs associated protein processing pathway endoplasmic reticulum. Notably, 8 specifically spikes contrasting spike-number germplasms, suggesting their potential role number regulation. This study provides high-quality resource identifies that may facilitate breeding enhanced .

Язык: Английский

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Cloning and Functional Study of AmGDSL1 in Agropyron mongolicum

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(17), С. 9467 - 9467

Опубликована: Авг. 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.

Язык: 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, Год журнала: 2024, Номер 306, С. 109136 - 109136

Опубликована: Ноя. 20, 2024

Язык: 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), Год журнала: 2024, Номер unknown

Опубликована: Дек. 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.

Язык: Английский

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

Briefings in Bioinformatics, Год журнала: 2024, Номер 26(1)

Опубликована: Ноя. 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.

Язык: Английский

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