BGRS: bioinformatics of genome regulation and data integration DOI Creative Commons
Yuriy L. Orlov, Ming Chen, Н. А. Колчанов

et al.

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, Journal Year: 2023, Volume and Issue: 20(3)

Published: Sept. 1, 2023

Gene expression regulation is one of the priority topics for bioinformatics development.The topic was background research areas Journal Integrative Bioinformatics [1,2].Experimental studies gene at transcription level led to development databases on factor -TRRD and TRANSFAC [3].The series tools binding sites prediction integrations has been developed [4][5][6].We have published papers such following rise high-throughput sequencing technologies corresponding growth experimental data [7,8].Integration resources databases, standardization exchange became separate field [9,10].Contemporary machine learning Big Data analysis methods serve solve same problems in much larger scale [4,11,12].Here we review current trends based material discussed BGRS∖SB (Bioinformatics Genome Regulation Structure∖Systems Biology) conference held Novosibirsk biannually.Recent meeting hold July 2022 (https://bgrssb.icgbio.ru/2022/).Previously had special collection from materials BGRS-2020 [2] earlier BGRS events [13][14][15].In year 2023, celebrate 25th anniversary Structure since 1998.As members Program committee, are happy remind history this great international conference.The first "Bioinformatics Structure/Systems Biology" (BGRS/SB) 1998, organized by science team Institute Cytology Genetics, Siberian Branch Russian Academy Sciences Conference Chairman Prof N. A. Kolchanov.At event just a small group scientists gathered Novosibirsk; they still remember exiting atmosphere hot discussions Altai mountains postconference trip 1998 (https://conf.icgbio.ru/bgrs98/committee/).BGRS longest-running biannual Russia gathering scientists, bioinformaticians, mathematicians IT-specialists, biophysicists, ecologists, medical doctors, geneticists (see video about 20th web-site).It grown relatively with less than 50 persons large multi-conference parallel sessions joining together up 500 participants different

Language: Английский

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity DOI Creative Commons
Ali Raza, Hajar Salehi, Shanza Bashir

et al.

Plant Cell Reports, Journal Year: 2024, Volume and Issue: 43(3)

Published: Feb. 27, 2024

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. widespread threat of can jeopardize global food security due to contaminated supplies pose environmental risks, contributing soil water pollution thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms combat stress. Amid array innovative approaches, omics, notably transcriptomics, proteomics, metabolomics, emerged as transformative tools, shedding light on genes, proteins, key metabolites involved stress responses tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, analytical pipelines support these omics approaches harnessing diverse information facilitating mapping genotype-to-phenotype relationships under conditions. This review explores: (1) multifaceted strategies that use adapt their environment; (2) latest findings metal(loid)-mediated metabolomics studies across various plant species; (3) integration data artificial intelligence high-throughput phenotyping; (4) bioinformatics single and/or multi-omics integration; (5) insights into adaptations future outlooks; (6) capacity advances creating sustainable resilient thrive metal(loid)-contaminated environments.

Language: Английский

Citations

23
Omics approaches in understanding the benefits of plant-microbe interactions DOI Creative Commons
Archana Jain, Surendra Sarsaiya,

Ranjan Singh

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: May 27, 2024

Plant-microbe interactions are pivotal for ecosystem dynamics and sustainable agriculture, influenced by various factors, such as host characteristics, environmental conditions, human activities. Omics technologies, including genomics, transcriptomics, proteomics, metabolomics, have revolutionized our understanding of these interactions. Genomics elucidates key genes, transcriptomics reveals gene expression dynamics, proteomics identifies essential proteins, metabolomics profiles small molecules, thereby offering a holistic perspective. This review synthesizes diverse microbial-plant interactions, showcasing the application omics in mechanisms, nitrogen fixation, systemic resistance induction, mycorrhizal association, pathogen-host Despite challenges data integration ethical considerations, approaches promise advancements precision intervention resilient agricultural practices. Future research should address challenges, enhance technology resolution, explore epigenomics, understand plant-microbe under conditions. In conclusion, technologies hold immense optimizing strategies fortifying alliances, paving way agriculture stewardship.

Language: Английский

Citations

16
Editorial: Applications of artificial intelligence, machine learning, and deep learning in plant breeding DOI Creative Commons

Maliheh Eftekhari,

Chuang Ma, Yuriy L. Orlov

et al.

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

Published: May 22, 2024

Editorial: Applications of artificial intelligence, machine learning, and deep learning in plant breeding

Language: Английский

Citations

5
The RAD6-like Ubiquitin Conjugase Gene OsUBC7 Has a Positive Role in the Early Cold Stress Tolerance Response of Rice DOI Open Access

Huy Phan,

Michael Schläppi

Genes, Journal Year: 2025, Volume and Issue: 16(1), P. 66 - 66

Published: Jan. 8, 2025

Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, elucidate genetic pathways involved in cold tolerance response mechanisms. We mapped OsUBC7, Radiation-sensitive 6 (RAD6)-type homolog of rice, low-temperature survivability (LTSS) QTL used genomics, molecular genetics, assays assess its role resilience against stress. OsUBC7 is responsive has higher expression levels cold-tolerant japonica than cold-sensitive indica. Overexpression enhances LTSS indica freezing Arabidopsis, increases soluble sugars chlorophyll A, boosts leaf development after exposure, cell numbers plants size, but it does not affect membrane stability exposure. Additionally, positive germinability the presence salt flowering yield-related traits. The protein physically interacts with developmental stage-specific histone-modifying E3 ligases OsRFPH2-12 OsHUB1/2, respectively, potential target genes such as cycle dependent kinases were identified. might contribute by regulating sugar metabolism provide energy promoting cellular homeostasis restoration exposure via new growth, particularly cells photosynthesis metabolic activity, possibly interacting proteins. Overall, present study suggests that may be development, reproduction, adaptation, contributes deeper understanding promising candidate improving crop productivity stressful environments.

Language: Английский

Citations

0
Utilizing modern techniques and omics technologies to enhance stress tolerance in finger millet, with recent findings: A review DOI Creative Commons
D. Yuvaraj,

J. Bevin Nishanth,

A. Premkumar

et al.

Food Chemistry Advances, Journal Year: 2025, Volume and Issue: 6, P. 100886 - 100886

Published: Jan. 11, 2025

Language: Английский

Citations

0
Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to Rhizoctonia solani under excess nitrogen fertilization using gene network reconstruction and analysis methods DOI Creative Commons
Е. А. Ощепкова, A. R. Volyanskaya,

A. V. Adamovskaya

et al.

Vavilov Journal of Genetics and Breeding, Journal Year: 2025, Volume and Issue: 28(8), P. 960 - 973

Published: Jan. 26, 2025

Although nitrogen fertilizers increase rice yield, their excess can impair plant resistance to diseases, particularly sheath blight caused by Rhizoctonia solani . This pathogen destroy up 50 % of the crop, but mechanisms underlying reduced under remain poorly understood. study aims identify potential marker genes enhance R. conditions. A comprehensive bioinformatics approach was applied, including differential gene expression analysis, network reconstruction, biological process overrepresentation phylostratigraphic and non-coding RNA co-expression analysis. The Smart crop cognitive system, ANDSystem, ncPlantDB database, other resources were used. Analysis molecular genetic interaction revealed three explaining nitrogen: OsGSK2-mediated pathway, OsMYB44-OsWRKY6-OsPR1 SOG1-Rad51-PR1/PR2 pathway. Potential markers for breeding identified: 7 controlling responses various stresses 11 modulating immune system. Special attention given key participants in regulatory pathways Non-coding analysis 30 miRNAs targeting reconstructed network. For two (Osa-miR396 Osa-miR7695), about 7,400 unique long RNAs (lncRNAs) with indices found. top lncRNAs highest index each miRNA highlighted, opening new perspectives studying pathogens. results provide a theoretical basis experimental work on creating varieties increased excessive nutrition. opens prospects developing innovative strategies aimed at optimizing balance between yield disease modern agrotechnical

Language: Английский

Citations

0
Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms DOI Creative Commons
M. A. Kleshchev,

Anastasia Maltseva,

Е. А. Ощепкова

et al.

Vavilov Journal of Genetics and Breeding, Journal Year: 2025, Volume and Issue: 28(8), P. 904 - 917

Published: Jan. 25, 2025

Drought is a critical factor limiting the productivity of bread wheat ( Triticum aestivum L.), one key agricultural crops. Wheat adaptation to water deficit ensured by complex molecular genetic mechanisms, including coordinated work multiple genes regulated transcription factors and signaling non-coding RNAs, particularly microRNAs (miRNAs). miRNA-mediated regulation gene expression considered main mechanisms plant resistance abiotic stresses. Studying these necessitates computational systems biology methods. This aims reconstruct analyze network associated with miRNA drought. Using ANDSystem software specialized Smart crop knowledge base adapted for genetics breeding, we reconstructed responding deficit, comprising 144 genes, 1,017 proteins, 21 miRNAs. Analysis revealed that miRNAs primarily regulate controlling morphogenesis shoots roots, crucial morphological The components are MYBa WRKY41 family factors, heat-shock protein HSP90, RPM1 protein. These proteins phytohormone pathways calcium-dependent kinases significant in adaptation. Several MIR7757 , MIR9653a MIR9671 MIR9672b ) were identified had not been previously discussed drought many nodes promising candidates experimental studies enhance deficiency. results obtained can find application breeding development new varieties increased which substantial importance agriculture context climate change.

Language: Английский

Citations

0
Advanced Strategies for Crop Improvement Against Abiotic Stresses: An Integrated View from Breeding to Genomics DOI

Jayanth Kallugudi,

Charu Lata,

R. Thribhuvan

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Can the molecular and transgenic breeding of crops be an alternative and sustainable technology to meet food demand? DOI
Celeste Gracia-Rodriguez,

Angela Elena Martínez-Medina,

Liliana Torres-Cosio

et al.

Functional & Integrative Genomics, Journal Year: 2025, Volume and Issue: 25(1)

Published: April 9, 2025

Language: Английский

Citations

0
Marker-Assisted Selection (MAS) Revolutionized: Integrating ‘Omics’ Data into Tomato Breeding DOI
Vidadala Rajendra

Published: Jan. 1, 2025

Language: Английский

Citations

0