Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15
Published: Dec. 9, 2024
Alders are widely distributed riparian trees in Europe, North Africa and Western Asia. Recently, a strong reduction of alder stands has been detected Europe due to infection by
Language: Английский
Genetics, Journal Year: 2024, Volume and Issue: 227(1)
Published: March 8, 2024
Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the thaliana genome. Its primary focus is integrating experimental gene function information from peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal to produce a "gold standard" functional annotation set that reflects current state of knowledge At same time, resource serves nexus for community-based collaborations aimed at improving quality, access, reuse. For past decade, our work made possible by subscriptions global user base. This update covers ongoing biocuration work, some modernization efforts contribute first major infrastructure overhaul since 2011, introduction JBrowse2, resource's role in community activities such organizing structural reannotation assessment, we used ontology annotations metric evaluate: (1) what currently known (2) "unknown" genes. Currently, 74% proteome annotated least one term. Of those loci, half have support following aspects: molecular function, biological process, or cellular component. sheds light on genes which not yet identified any published no annotation. Drawing attention these unknown highlights gaps potential sources novel discoveries.
Language: Английский
Citations
76
GigaScience, Journal Year: 2025, Volume and Issue: 14
Published: Jan. 1, 2025
The scientific community has long benefited from the opportunities provided by data reuse. Recognizing need to identify challenges and bottlenecks reuse in agricultural research propose solutions for them, working group was started within AgBioData consortium framework. Here, we limitations of standards, metadata deficiencies, interoperability, ownership, availability, user skill level, resource equity issues, with a specific focus on genomics research. We possible stakeholders could implement mitigate overcome these provide an optimistic perspective future transcriptomics
Language: Английский
Citations
2
Biomolecules, Journal Year: 2023, Volume and Issue: 13(9), P. 1403 - 1403
Published: Sept. 17, 2023
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution build clade-specific pan-genomes several crops. crops constructed various cultivars, accessions, landraces, wild ancestral represent compendium genes structural variations allow researchers search for the novel alleles that were inadvertently lost in domesticated during historical process crop domestication or extensive plant breeding. Fortunately, many valuable associated with desirable traits like disease resistance, abiotic stress tolerance, architecture, nutrition qualities exist species, relatives. ancestors landraces can be introduced back high-yielding varieties modern by implementing classical breeding, selection, transgenic/gene editing approaches. Thus, pan-genomic represents great leap research offers new avenues targeted breeding mitigate impact global climate change. Here, we summarize tools used pan-genome assembly annotations, web-portals hosting pan-genomes, etc. Furthermore, highlight few discoveries using approach future potential this emerging field study.
Language: Английский
Citations
12
Current Opinion in Plant Biology, Journal Year: 2025, Volume and Issue: 83, P. 102684 - 102684
Published: Jan. 5, 2025
Language: Английский
Citations
0
Database, Journal Year: 2025, Volume and Issue: 2025
Published: Jan. 1, 2025
Abstract Advances in agricultural genetic, genomic, and breeding (GGB) technologies generate increasingly large complex datasets that need to be adequately managed shared. While several biological databases maintain curate GGB data, not all scientists are aware of them how they can used access share data. In addition, there is the increase scientists’ awareness appropriate data archiving curation increases longevity value bolsters scientific discoveries’ reproducibility transparency. The AgBioData Education working group aims address these unmet needs developed a modular curriculum for educators teaching basics findable, accessible, interoperable, reusable (FAIR) principles undergraduate graduate students (https://www.agbiodata.org/). present paper provides an overview topics covered within curriculum, called ‘AgBioData Curriculum Ag FAIR Data,’ its audience modalities, it will positively impact different stakeholders database ecosystem. We hope presented here help understand support use aspects improving our global food system. Database URL: https://zenodo.org/records/14278084
Language: Английский
Citations
0
Engineering, Journal Year: 2024, Volume and Issue: unknown
Published: June 1, 2024
Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional genomics, digital breeding, and smart cultivation. Despite this advancement, lack of standards creation usage technology equipment become a bottleneck, limiting industry's high-quality development. This paper begins with an overview phenotyping industry presents industrial mapping big data phenomics. It analyzes necessity current state constructing standard framework phenotyping. Furthermore, proposes intended organizational structure goals framework. details essentials research development hardware equipment, acquisition, storage management data. Finally, it discusses promoting construction evaluation framework, aiming provide ideas developing
Language: Английский
Citations
3
Frontiers in Sustainable Food Systems, Journal Year: 2024, Volume and Issue: 8
Published: May 24, 2024
Implementing a cropping intensity program with rice cultivation four times year (CI 400) can be achieved using early maturing varieties of rice. However, this development needs to pay attention the adaptability planted ensure successful implementation. The approach is combination assessing stability and productivity potential. This concept has been developed applied in several studies, including research on considered less comprehensive because it non-parametric only focuses one analysis. Therefore, systematic integration various analyses, index methods, needed comprehensively assess adaptability, particularly for early-maturing South Sulawesi. region characterized by dynamic climate zone top highest producers Indonesia. Meanwhile, study aims develop select best varieties, especially investigation was conducted Bone, Soppeng, Gowa over two seasons nested randomized complete block design, organized replications each environment (location-season). Additionally, there significant focus application five check factor repeated three at location, totaling 126 experimental units. results showed that index, combining rank accumulation yield min max standardization, effective potential supporting CI 400. Inpari 13 had value 0.55, followed Cakrabuana 0.31; hence both were recommended as adaptive
Language: Английский
Citations
2
Plants People Planet, Journal Year: 2024, Volume and Issue: 7(1), P. 23 - 32
Published: Sept. 12, 2024
Societal Impact Statement Genebanks contribute to global food security, directly influencing societal well‐being, by providing access seed or genetic material that is more resilient pests, diseases, and environmental stresses. The ability develop crops adapted changing conditions with high nutritional value means societies can better cope the adverse effects of climate change, safeguarding production rural livelihoods. Enhancing sustainable crop traits, such as improved water‐use efficiency nutrient utilization, supports transition toward agricultural practices. New technologically advanced phenotyping tools are required optimally realize potential these resources, identify plant resources will best enable us address current challenges. Summary Plant genebanks have a crucial role specialized repositories, preserving diverse essential researchers, breeders, farmers for developing crops. With over 7 million accessions, significantly change mitigation, agriculture. This opinion paper, inspired an international workshop in 2022 Wageningen (Netherlands), focuses on transformative impact phenomics technology within genebanks, offering view its applications implications utilizing resources. Discussions from organized International Phenotyping Network integrated, emphasizing collaboration without requiring major policy developments. prioritized traits like disease resistance drought tolerance, highlighting roots critical organ phenotyping. Participants expressed keen interest collaboration, need partnerships between facilities. workshop's outcomes underscore promoting innovation, These results guide future pilot studies, marking significant step integrating into genebank practices ensuring continued prosperity heritage.
Language: Английский
Citations
2
Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1538 - D1547
Published: Nov. 20, 2023
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based projections to 129 additional species, spanning single-cell photoautotrophs, non-vascular plants, higher thus encompassing wide-ranging taxonomic diversity. Currently, houses collection of 339 pathways, covering metabolic transport hormone signaling, genetic regulations developmental processes, intricate transcriptional networks that orchestrate plant's response abiotic biotic stimuli. Beyond being mere repository, serves as dynamic data discovery platform. Users can analyze visualize omics data, such gene expression, gene-gene interaction, proteome, metabolome all within the rich context pathways. dedicated fostering interoperability, upholding global standards, embracing tenets Findable, Accessible, Interoperable Re-usable (FAIR) policy.
Language: Английский
Citations
4
Published: Jan. 10, 2024
The scientific community has long benefited from the opportunities provided by data reuse. Recognizing need to identify challenges and bottlenecks reuse in agricultural research propose solutions for them, working group was started within AgBioData consortium (https://www.agbiodata.org/) framework. Here, we limitations of standards, metadata deficiencies, interoperability, ownership, availability, user skill level, resource equity issues, with a specific focus on genomics research. We possible stakeholders could implement mitigate overcome these provide an optimistic perspective future transcriptomics
Language: Английский
Citations
1