Bioinformatics Approaches in Plant Physiology DOI
Mehmet Emin Uras

BENTHAM SCIENCE PUBLISHERS eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 239 - 261

Published: Dec. 18, 2024

Bioinformatics has proven to be a powerful tool in enhancing productivity across various fields, including plant biology. provides significant capabilities for the acquisition, processing, analysis, and interpretation of large amounts genomic data. With help next-generation sequencing technologies, genetic data can generated rapidly. The integration bioinformatics tools into physiology allows analysis information, providing better understanding functional aspects developmental, metabolic, reproductive processes. Moreover, it offers scientific framework pre-experimental planning, in-experimental management, post-experimental analysis. key applications comprise gene pathway identification, molecular docking, sequence RNA protein prediction, expression protein-protein interaction statistical techniques that executed from genome phenome. In order enhance plants, may play crucial role encouraging public release all through repositories, rationally annotating genes, proteins, phenotypes, elucidating links between many components potential facilitate crop improvement, and/or development new plant-based chemicals biofortified foods plants are more resistant stress conditions. Therefore, this contributes comprehensive areas These approaches include pan-genomics, artificial intelligence, machine deep learning applications, CRISPR technology editing, single-cell sequencing, third-generation systems, engineering post-transcriptional metagenomic studies. This chapter reviews methods biological databases their contributions physiology.

Language: Английский

Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption DOI Creative Commons
Hong Yang,

Yuting Cui,

Yanrong Feng

et al.

Cells, Journal Year: 2023, Volume and Issue: 12(5), P. 729 - 729

Published: Feb. 24, 2023

Abiotic stresses triggered by climate change and human activity cause substantial agricultural environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, regulation of transcription translation. Over the past decade, a large body literature has revealed various regulatory roles long non-coding RNAs (lncRNAs) their irreplaceable functions adaptation. LncRNAs are recognized class ncRNAs that longer than 200 nucleotides, influencing variety biological processes. In this review, we mainly focused on recent progress lncRNAs, outlining features, evolution, lncRNAs drought, low or high temperature, salt, heavy metal stress. The approaches characterize function how they regulate responses were further reviewed. Moreover, discuss accumulating discoveries regarding memory well. present review provides updated information directions for us potential future.

Language: Английский

Citations

46
Integrating omics databases for enhanced crop breeding DOI Creative Commons
Haoyu Chao, Shilong Zhang, Yueming Hu

et al.

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, Journal Year: 2023, Volume and Issue: 20(4)

Published: July 24, 2023

Abstract Crop plant breeding involves selecting and developing new varieties with desirable traits such as increased yield, improved disease resistance, enhanced nutritional value. With the development of high-throughput technologies, genomics, transcriptomics, metabolomics, crop has entered a era. However, to effectively use these integration multi-omics data from different databases is required. Integration omics provides comprehensive understanding biological processes underlying their interactions. This review highlights importance integrating in breeding, discusses available databases, describes challenges, recent developments potential benefits. Taken together, critical step towards enhancing improving global food security.

Language: Английский

Citations

26
Plant non-coding RNAs function in pollen development and male sterility DOI Creative Commons
Hushuai Nie, Cheng Cheng, Jie Kong

et al.

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

Published: Feb. 15, 2023

Male sterility is classified as either cytoplasmic male (CMS) or genic (GMS). Generally, CMS involves mitochondrial genomes interacting with the nuclear genome, while GMS caused by genes alone. regulated multilevel mechanisms in which non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long (lncRNAs), and phased small interfering (phasiRNAs), have been proven to be critical elements. The development of high-throughput sequencing technology offers new opportunities evaluate genetic mechanism ncRNAs plant sterility. In this review, we summarize that regulate gene expression ways dependent on independent hormones, involve differentiation stamen primordia, degradation tapetum, formation microspores, release pollen. addition, key miRNA–lncRNA–mRNA interaction networks mediating plants are elaborated. We present a different perspective exploring ncRNA-mediated regulatory pathways control create male-sterile lines through hormones genome editing. A refined understanding ncRNA for sterile would conducive improve hybridization breeding.

Language: Английский

Citations

21
The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research DOI
Luis Alberto Bravo-Vázquez,

Andrea Méndez-García,

Verenice Chamu-García

et al.

Planta, Journal Year: 2023, Volume and Issue: 259(2)

Published: Dec. 28, 2023

Language: Английский

Citations

12
Interactions between lncRNAs and cyclins/CDKs complexes; key players in determining cancer cell response to CDKs inhibitors DOI

Bahaa Ibrahim Saeed,

Abhinav Kumar, Enwa Felix Oghenemaro

et al.

Experimental Cell Research, Journal Year: 2025, Volume and Issue: 445(2), P. 114406 - 114406

Published: Jan. 4, 2025

Language: Английский

Citations

0
Noncoding RNAs properties and biological functions in plant development and abiotic stress response DOI

Aiswarya Rajasekharan

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 203 - 216

Published: Jan. 1, 2025

Language: Английский

Citations

0
Exploring the critical role of non-coding RNAs in plant development and stress adaptation-current status and insights DOI
Nilesh Shirish Wagh,

Pranav Amane,

R. V. Kshirsagar

et al.

Progress in molecular biology and translational science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology DOI Creative Commons
Luis Alberto Bravo-Vázquez, Ana Marta Castro-Pacheco,

Rodrigo Pérez-Vargas

et al.

Non-Coding RNA, Journal Year: 2025, Volume and Issue: 11(2), P. 19 - 19

Published: March 2, 2025

Improving crop yield potential is crucial to meet the increasing demands of a rapidly expanding global population in an ever-changing and challenging environment. Therefore, different technological approaches have been proposed over last decades accelerate plant breeding. Among them, artificial microRNAs (amiRNAs) represent innovative tool with remarkable assist improvement. MicroRNAs (miRNAs) are group endogenous, small (20-24 nucleotides), non-coding RNA molecules that play role gene regulation. They associated most biological processes plant, including reproduction, development, cell differentiation, biotic abiotic stress responses, metabolism, architecture. In this context, amiRNAs synthetic engineered mimic structure function endogenous miRNAs, allowing for targeted silencing specific nucleic acids. The current review explores diverse applications biology agriculture, such as management infectious agents pests, engineering enhancement resilience stress. Moreover, we address future perspectives on amiRNA-based strategies, highlighting need further research fully comprehend technology translate its scope toward widespread adoption strategies

Language: Английский

Citations

0
Non-coding RNAs: emerging biomarkers and therapeutic targets in cancer and inflammatory diseases DOI Creative Commons
Basma Hossam Abdelmonem,

Lereen T. Kamal,

Lilian Waheed Wardy

et al.

Frontiers in Oncology, Journal Year: 2025, Volume and Issue: 15

Published: March 10, 2025

Non-coding RNAs (ncRNAs) have a significant role in gene regulation, especially cancer and inflammatory diseases. ncRNAs, such as microRNA, long non-coding RNAs, circular alter the transcriptional, post-transcriptional, epigenetic expression levels. These molecules act biomarkers possible therapeutic targets because aberrant ncRNA has been directly connected to tumor progression, metastasis, response therapy research. ncRNAs’ interactions with multiple cellular pathways, including MAPK, Wnt, PI3K/AKT/mTOR, impact processes like proliferation, apoptosis, immune responses. The potential of RNA-based therapeutics, anti-microRNA microRNA mimics, restore normal is being actively studied. Additionally, tissue-specific patterns ncRNAs offer unique opportunities for targeted therapy. Specificity, stability, responses are obstacles use ncRNAs; however, novel strategies, modified oligonucleotides delivery systems, developed. profiling may result more individualized successful treatments precision medicine advances, improving patient outcomes creating early diagnosis monitoring opportunities. current review aims investigate roles diseases, focusing on their mechanisms regulation implications non-invasive diagnostics therapies. A comprehensive literature was conducted using PubMed Google Scholar, research published between 2014 2025. Studies were selected based rigorous inclusion criteria, peer-reviewed status relevance Non-English, non-peer-reviewed, inconclusive studies excluded. This approach ensures that findings presented high-quality relevant sources.

Language: Английский

Citations

0
A Bread Wheat Line with the Substituted Wild Emmer Chromosome 4A Results in Fragment Deletions of Chromosome 4B and Weak Plants DOI Creative Commons
Yu Qiu, Fei Lu, Bai Yang

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(7), P. 1134 - 1134

Published: April 5, 2025

In response to the growing genetic uniformity within wheat populations, developing efficient wheat-alien translocation strategies has become critically important. We observed that several offspring of common (Triticum aestivum L.)-wild emmer turgidum L. var. dicoccoides) chromosome arm substitution line (CASL4AL) exhibited stunted growth, including significantly reduced plant height, spike length, spikelet number, and stem width compared normal plants. Integrative transcriptomic analyses (RNA-Seq BSR-Seq) revealed a statistically significant depletion (p < 0.01) single nucleotide polymorphisms (SNPs) on 4B in compromised Chromosome association analysis differentially expressed genes (DEGs, up- or downregulated) downregulated were predominantly located 4B. The 1244 DEGs Chr4B employed for Gene Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) analyses, RNA metabolic processes, DNA repair, transport systems enriched by GO analysis; however, only mRNA surveillance pathway was KEGG enrichment. Molecular marker profiling showed complete absence target amplification critical 0-155 Mb region all weak Pearson's correlation coefficients confirmed associations between 4B-specific phenotypes. These results demonstrate segmental deletions drive phenotypes CASL4AL progeny, provide experimental evidence induced wild lines. This study highlights potential as valuable tool generating chromosomal variations breeding programs.

Language: Английский

Citations

0