BnIR: A multi-omics database with various tools for Brassica napus research and breeding

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(4), P. 775 - 789

Published: March 14, 2023

In the post-genome-wide association study era, multi-omics techniques have shown great power and potential for candidate gene mining functional genomics research. However, due to lack of effective data integration analysis platforms, such not still been applied widely in rapeseed, an important oil crop worldwide. Here, we report a rapeseed database (BnIR; http://yanglab.hzau.edu.cn/BnIR), which provides datasets six omics including genomics, transcriptomics, variomics, epigenetics, phenomics, metabolomics, as well numerous "variation-gene expression-phenotype" associations by using multiple statistical methods. addition, series search tools are integrated facilitate browsing application these datasets. BnIR is most comprehensive so far, two case studies demonstrated its mine genes associated with specific traits analyze their regulatory mechanisms.

Language: Английский

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Machine learning bridges omics sciences and plant breeding

Trends in Plant Science, Journal Year: 2022, Volume and Issue: 28(2), P. 199 - 210

Published: Sept. 21, 2022

Language: Английский

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Fecal microbiota transplantation: current challenges and future landscapes

Clinical Microbiology Reviews, Journal Year: 2024, Volume and Issue: 37(2)

Published: May 8, 2024

SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest developing innovative therapeutic strategies for restoring microbiota. One such approach, fecal microbiota transplantation (FMT), is main "whole microbiome replacement" strategy and integrated into clinical practice guidelines treating recurrent

Language: Английский

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Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams

iMeta, Journal Year: 2024, Volume and Issue: 3(3)

Published: April 11, 2024

Abstract Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such metabolomics, genomics, transcriptomics, and proteomics, utility is undeniable. However, the operational complexity has been compounded by absence standardized data formats need switch between various platforms generating different diagrams. To address these challenges, we introduce EVenn platform, a versatile tool offering unified interface efficient exploration visualization ( http://www.ehbio.com/test/venn ) streamlines upload process with format, enhancing capabilities multimodule analysis. This comprehensive protocol outlines applications EVenn, featuring representative results multiple diagrams, uploads in centralized center, step‐by‐step case demonstrations. Through functionalities, emerges valuable user‐friendly in‐depth multiomics data.

Language: Английский

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Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

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

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Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 17, 2025

The innovations of the "Omics Era" have ushered in significant advancements genetic improvement agriculturally important animal species through transforming genetics, genomics and breeding strategies. These were often coordinated, part, by support provided over 30 years 1993-2023 National Research Support Project 8 (NRSP8, Animal Genome Program, NAGRP) affiliate projects focused on enabling genomic discoveries livestock, poultry, aquaculture species. parallel advances demand strategic planning future research priorities. This paper, as an output from May 2023 Aquaculture Genomics, Genetics, Breeding Workshop, provides updated status resources for United States species, highlighting major achievements emerging Finfish shellfish genome omics enhance our understanding architecture heritability performance production traits. Workshop identified present aims genomics/omics to build this progress: (1) advancing reference assembly quality; (2) integrating multi-omics data analysis traits; (3) developing collection integration phenomics data; (4) creating pathways applying information across industries; (5) providing training, extension, outreach application phenome. focuses should emphasize collection, artificial intelligence, identifying causative relationships between genotypes phenotypes, establishing apply tools industries, expansion training programs next-generation workforce facilitate sciences into operations productivity, competitiveness, sustainability. collective vision with focus highlighted priorities is intended continued advancement genomics, genetics community industries. Critical challenges ahead include practical analytical frameworks beyond academic communities that require collaborative partnerships academia, government, industry. scope review encompasses use applications study aquatic animals cultivated human consumption settings throughout their life-cycle.

Language: Английский

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Unsupervised and semi‐supervised learning: the next frontier in machine learning for plant systems biology

The Plant Journal, Journal Year: 2022, Volume and Issue: 111(6), P. 1527 - 1538

Published: July 13, 2022

SUMMARY Advances in high‐throughput omics technologies are leading plant biology research into the era of big data. Machine learning (ML) performs an important role systems because its excellent performance and wide application analysis However, to achieve ideal performance, supervised ML algorithms require large numbers labeled samples as training In some cases, it is impossible or prohibitively expensive obtain enough data; here, paradigms unsupervised (UL) semi‐supervised (SSL) play indispensable role. this review, we first introduce basic concepts techniques, well representative UL SSL algorithms, including clustering, dimensionality reduction, self‐supervised (self‐SL), positive‐unlabeled (PU) transfer learning. We then review recent advances applications both phenotyping research. Finally, discuss limitations highlight significance challenges strategies biology.

Language: Английский

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Molecular Breeding and Drought Tolerance in Chickpea

Life, Journal Year: 2022, Volume and Issue: 12(11), P. 1846 - 1846

Published: Nov. 11, 2022

L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to Leguminosae family. Drought utmost common abiotic factor on plants, distressing their water status limiting growth development. Chickpea genotypes have natural ability fight drought stress using certain strategies viz., escape, avoidance tolerance. Assorted breeding methods, including hybridization, mutation, marker-aided breeding, genome sequencing along with omics approaches, could be used improve chickpea germplasm lines(s) against stress. Root features, for instance depth root biomass, been recognized as beneficial morphological factors managing terminal tolerance in chickpea. Marker-aided selection, example, a genomics-assisted (GAB) strategy that can considerably increase accuracy competence. These technologies, notably marker-assisted omics, plant physiology knowledge, underlined importance of future improvement programmes generate drought-tolerant cultivars(s).

Language: Английский

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Multi-omics revolution to promote plant breeding efficiency

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 8, 2022

Crop production is the primary goal of agricultural activities, which always taken into consideration. However, global systems are coming under increasing pressure from rising food demand rapidly growing world population and changing climate. To address these issues, improving high-yield climate-resilient related-traits in crop breeding an effective strategy. In recent years, advances omics techniques, including genomics, transcriptomics, proteomics, metabolomics, paved way for accelerating plant/crop to cope with climate enhance production. Optimized phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid development biological interpretations complex traits. The precise progressive assembly desire alleles using genome editing approaches enhanced strategies would enable future crops excel combating climates. Furthermore, plant genetic engineering ensures exclusive approach developing nutrient sufficient crops, productivity can sustainably adequately meet world's food, nutrition, energy needs. This review provides overview how integration could be select varieties desired

Language: Английский

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Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(19), P. 12053 - 12053

Published: Oct. 10, 2022

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops not tolerant climatic environments. aim near future, a world with hunger an population, breed and/or engineer tolerate abiotic stress higher yield. Some crop varieties display certain degree of tolerance, which has been exploited by plant breeders develop thrive under conditions. Moreover, long list genes involved tolerance have identified characterized molecular techniques overexpressed individually transformation experiments. Nevertheless, phenotypes polygenetic traits, current genomic tools dissecting exploit their use accelerating genetic introgression using markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe mechanisms sense adverse conditions examine discuss classic new select improve crops.

Language: Английский

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