Comprehensive insights into herbicide resistance mechanisms in weeds: a synergistic integration of transcriptomic and metabolomic analyses DOI Creative Commons
Madhab Kumar Sen, Soham Bhattacharya, Rohit Bharati

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 11, 2023

Omics techniques, including genomics, transcriptomics, proteomics, and metabolomics have smoothed the researcher’s ability to generate hypotheses discover various agronomically relevant functions mechanisms, as well their implications associations. With a significant increase in number of cases with resistance multiple herbicide modes action, studies on are currently one predominant areas research within field weed science. High-throughput technologies already started revolutionizing current molecular biology studies. The evolution weeds (particularly via non-target site mechanism) is perfect example complex, multi-pathway integration-induced response. To date, functional transcriptomic metabolomic been used separately research, however there substantial lack integrated approach. Hence, despite omics provide insights into functioning weeds, using single can sometimes be misleading. This mini-review will aim discuss progress transcriptome-based metabolome-based approaches along systematic integration.

Language: Английский

Cold-stress induced metabolomic and transcriptomic changes in leaves of three mango varieties with different cold tolerance DOI Creative Commons
Yu Kong,

Xianbin Hou,

Zhenglu Liu

et al.

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

Published: April 10, 2024

Mango (Mangifera indica L.) is grown in Hainan, Guangdong, Yunnan, Sichuan, and Fujian provinces Guanxi autonomous region of China. However, trees growing these areas suffer severe cold stress during winter, which affects the yield. To this regard, data on global metabolome transcriptome profiles leaves are limited. Here, we used combined analyses three mango cultivars with different tolerance, i.e. Jinhuang (J)-tolerant, Tainung (T) Guiremang No. 82 (G)-susceptible, after 24 (LF), 48 (MF) 72 (HF) hours cold.

Language: Английский

Citations

6
A chromosome-scale genome assembly of Malus domestica, a multi-stress resistant apple variety DOI Creative Commons
Sijun Qin, Gongxun Xu,

Jiali He

et al.

Genomics, Journal Year: 2023, Volume and Issue: 115(3), P. 110627 - 110627

Published: April 14, 2023

Hanfu apple is the main cultivar grown in cool areas of Northeast, Northwest, and North China. Here, we proposed a chromosome-level genome assembly using PacBio, Illumina Hi-C sequencing data. The total contig length was 628.99 Mb, with scaffold N50 sizes 36.18 Mb 1.25 respectively. had 39,617 genes, which predicted function for 38,816. Evolutionary analysis showed that may have undergone γ-event, recent whole-genome duplication. A comparative conducted on genomes homozygous triploid HFTH1, were cultured anthers diploid apples. Three variants identified, including 2,155,184 single nucleotide polymorphisms (SNPs), 413,108 insertions/deletions (indels), 7,587 structural (SVs).This high-quality will provide reference genetic improvement apples breeding more varieties high resistance quality.

Language: Английский

Citations

12
Integrated transcriptomics and metabolomics analyses reveal key genes and essential metabolic pathways for the acquisition of cold tolerance during dormancy in apple DOI Creative Commons
Gongxun Xu, Lijie Li, Jia Zhou

et al.

Environmental and Experimental Botany, Journal Year: 2023, Volume and Issue: 213, P. 105413 - 105413

Published: June 16, 2023

Low temperature is a primary abiotic stress that significantly affects plant growth and development in the cool regions of Northeast China. It limiting factor global apple industry. Numerous studies have investigated alterations transcriptional metabolism under low-temperature various plants. However, research on role dormancy regulating differences cold tolerance among varieties limited. Therefore, this study conducted comprehensive analysis physiological biochemical indices, transcriptome, metabolome cold-tolerant variety 'Hanfu' (HF) cold-sensitive 'Naganofuji 2′ (CF) during endodormancy ecodormancy. Under treatment, cross-section 1-year-old branch CF exhibited more severe browning than HF did, relative electrolyte leakage value was higher HF. Transcriptomics metabolomics revealed key pathways apples response to stress. Functional enrichment showed hormone signal transduction amino acid metabolism-related were enriched ecodormancy, these considered an important way for respond freezing injury. The galactose pathway only endodormancy, while membrane lipid A gene co-expression network constructed using weighted correlation analysis, six modules with biological significance selected from network. Among them, genes encoding transcription factors such as DREB1C/CBF2, JUB1, CCCH, VIP1 are hub different modules, which can be used candidate explore regulation Overall, findings help elucidate molecular mechanism underlying freeze-tolerance provide novel insights into regulatory involved dormancy.

Language: Английский

Citations

10
Integrated morpho-physiological, transcriptomic and metabolomic data to reveal the differential chilling defense mechanisms of two ecologically diverged species of Forsythia DOI Creative Commons
Jian Cui, Rong Wu, Xiaoyang Sun

et al.

Horticultural Plant Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
Widely Targeted Metabolomics and Transcriptomics Analysis of the Response and Adaptation Mechanisms of Trifolium ambiguum to Low-Temperature Stress DOI Creative Commons

Kefan Cao,

Sijing Wang, Huimin Zhang

et al.

Agronomy, Journal Year: 2025, Volume and Issue: 15(2), P. 308 - 308

Published: Jan. 26, 2025

Caucasian clover (Trifolium ambiguum M.Bieb.) is a perennial legume known for its exceptional cold tolerance, commonly used in agriculture and ecosystems climates. Given the impact of climate change, enhancing adaptation crucial sustaining agricultural productivity. This study employs metabolomics, transcriptomics, Weighted Gene Co-expression Network Analysis (WGCNA) to investigate molecular mechanisms clover’s response low-temperature stress. Metabolomic analysis showed that stress triggered accumulation fatty acids, amino antioxidants, which are critical maintaining membrane stability antioxidant capacity, thus protecting plant from oxidative damage. Transcriptomic revealed significant upregulation genes involved adaptation, particularly those related defense, lipid repair, signal transduction, including ABA signaling pathway enzymes, thereby improving tolerance. WGCNA identified gene modules closely linked especially acid metabolism, repair. These function synergistically, with coordinated expression resistance. also investigated isoflavonoid biosynthesis under stress, highlighting role capacity Low-temperature induced key enzyme genes, such as Isoflavone Synthase (IFS) Isoflavone-7-O-Glucosyltransferase (IF7GT), promoting metabolite further plant’s adaptation. Overall, this offers novel insights into tolerance provides valuable theoretical support breeding cold-resistant crops

Language: Английский

Citations

0
Integrative Profiling of Phytohormones, Metabolomics, and Transcriptomics Reveals Key Regulators of Cold Tolerance in Cucumber Leaves DOI Creative Commons
Shijun Sun,

Shuiyuan Hao,

Ye Liu

et al.

Food Science & Nutrition, Journal Year: 2025, Volume and Issue: 13(3)

Published: March 1, 2025

A low-temperature condition in a root zone is major abiotic stress that threatens cucumber (Cucumis sativus L.) growth and development, yet the molecular mechanism by which leaf reacts to chilling remains largely unknown. In this study, we applied three temperature treatments, including room (20°C-22°C), suboptimal (13°C-15°C), low (8°C-10°C), investigate how affects hormone dynamics, metabolomics, transcriptomics leaves of variety "Jinyou 35", main cultivar northwest southwest China. Through integrative physiological biochemical analysis, auxin emerges as most significant accumulated hormone, accounting for 88% temperature-treated (RL), 99% (SL), 94% low-temperature-treated (LL). Under stress, flavanones were abundant metabolite leaves, constituting over 50% total metabolites, while phenolic acids showed marked decrease. Several differentially expressed transcription factors (DETFs), such LOB (CsaV3_3G020650), MYB (CsaV3_3G043510), bHLH (CsaV3_2G005070 CsaV3_4G029740), upregulated SL LL, potentially enhancing cucumber's defense against injury. Additionally, terminal flower formation was observed under conditions, with CsFT expression LL lower than RL, negative correlation between CsNAC6. These findings deepen our understanding resilience mechanisms shedding light on its cold tolerance strategies.

Language: Английский

Citations

0
Effects of bleeding on stem physiology of Actinidia arguta (Sieb. & Zucc) Planch. ex miq. and metabolomics analysis of bleeding sap DOI
Yaxuan Jiang,

Pei Lei,

Jianxin Li

et al.

Plant Physiology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109835 - 109835

Published: March 1, 2025

Language: Английский

Citations

0
Reprogramming of Metabolome and Transcriptome Shaped the Elevational Adaptation of Quercus variabilis by Regulating Leaf Functional Traits DOI

Hai-wei Zhang,

Yaru Wang,

Jieyan Yang

et al.

Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown

Published: May 5, 2025

ABSTRACT Exploring how plants adapt to environmental changes is key plant survive and protection under accelerating climate change. Quercus variabilis widely distributed in China with high economic ecological value, yet its elevational adaptation mechanism remains unclear. Here, we investigated the leaf functional traits, metabolome transcriptome of Q. along an gradient (800–1400 m) Mt. Li, China. Results showed that leaves at higher elevations became smaller, narrower, thicker, smaller denser stomata, maintained levels nitrogen, soluble sugar, total phenol, lignin sugar‐to‐starch ratio. With increasing elevation, underwent a metabolic shift from being dominated by primary metabolism secondary metabolism, 1300 m could be identified as transition point. Particularly, phenylpropanoid metabolites (flavonoids phenolic acids) played crucial roles elevations. Moreover, 24 hub transcription factors (TFs) were screened through WGCNA verified RT‐qPCR. Environmental not only directly influenced but also affected metabolite accumulation TF‐mediated gene expression, which turn traits. This study highlights integrating simultaneously provides novel insights into mechanisms for shaping plants’ adaptability.

Language: Английский

Citations

0
Nitric oxide production, sugar metabolism, and antioxidant capacity related to differential cold tolerance and recovery between two Dichondra repens genotypes DOI Creative Commons
Yao Ling,

Junnan Lin,

Dandan Peng

et al.

Industrial Crops and Products, Journal Year: 2025, Volume and Issue: 231, P. 121132 - 121132

Published: May 14, 2025

Language: Английский

Citations

0
Genome‐wide identification of XTH gene family in Musa acuminata and response analyses of MaXTHs and xyloglucan to low temperature DOI

Yehuan Tan,

Huiling Zhan,

Houbin Chen

et al.

Physiologia Plantarum, Journal Year: 2024, Volume and Issue: 176(2)

Published: Feb. 29, 2024

Abstract Banana ( Musa spp.) production is seriously threatened by low temperature (LT) in tropical and subtropical regions. Xyloglucan endotransglycosylase/hydrolases (XTHs) are considered chief enzymes cell wall remodelling play a central role stress responses. However, whether MaXTHs involved the tolerance banana not clear. Here, identification characterization of were carried out, followed prediction their cis‐acting elements protein–protein interactions. In addition, candidate to LT screened through comparison responses between tolerant sensitive cultivars using RNA‐Seq analysis. Moreover, immunofluorescence (IF) labelling was employed compare changes temporal spatial distribution different types xyloglucan components these two upon stress. total, 53 have been identified, all predicted be located wall, 14 them also cytoplasm. Only 11 found interact with other proteins. Among 16 responsiveness elements, MaXTH26/29/32/35/50 (Group I/II members) MaXTH7/8 IIIB might IF results suggested that content recognized CCRC‐M87/103/104/106 antibodies negatively related chilling tolerance. conclusion, we identified MaXTH gene family assessed re‐modelling under These will beneficial for breeding against stresses enrich wall‐mediated resistance mechanism plants stresses.

Language: Английский

Citations

3