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Abstract Advances in agricultural genetic, genomic, and breeding (GGB) technologies generate increasingly large and complex datasets that need to be adequately managed and shared. While several agricultural biological databases maintain and curate GGB data, not all scientists are aware of them and how they can be used to access and share data. In addition, there is the need to increase scientists’ awareness that appropriate data archiving and curation increases data longevity and value and bolsters scientific discoveries’ reproducibility and transparency. The AgBioData Education working group aims to address these unmet needs and developed a modular curriculum for educators teaching the basics of biological databases and the findable, accessible, interoperable, and reusable (FAIR) principles to undergraduate and graduate students (https://www.agbiodata.org/). The present paper provides an overview of the topics covered within the curriculum, called ‘AgBioData Curriculum for Ag FAIR Data,’ its audience and modalities, and how it will positively impact all the different stakeholders of the agricultural database ecosystem. We hope the modular curriculum presented here can help scientists and students understand and support database use in all aspects of improving our global food system. Database URL: https://zenodo.org/records/14278084 

An unwelcoming climate and culture at scientific conferences is an obstacle to retaining scientists with marginalized identities. Here we describe how a number of professional societies in the plant sciences, mostly based in the United States, collaborated on a project called ROOT & SHOOT (short for Rooting Out Oppression Together and SHaring Our Outcomes Transparently) to make conferences in the field more inclusive. The guidelines we developed, and our efforts to implement them in 2023 and 2024, are summarized here to assist other conference organizers with creating more inclusive conferences. 

Abstract Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021–22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org. 

Abstract Background The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Findings Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Conclusion Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.