Source: WASHINGTON STATE UNIVERSITY submitted to NRP
ENABLING GENOMICS-ASSISTED SPECIALTY CROP BREEDING AND RESEARCH THROUGH ADVANCED DATABASE RESOURCES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1029319
Grant No.
2022-51181-38449
Cumulative Award Amt.
$5,176,559.00
Proposal No.
2022-05305
Multistate No.
(N/A)
Project Start Date
Sep 15, 2022
Project End Date
Sep 14, 2026
Grant Year
2022
Program Code
[SCRI]- Specialty Crop Research Initiative
Recipient Organization
WASHINGTON STATE UNIVERSITY
240 FRENCH ADMINISTRATION BLDG
PULLMAN,WA 99164-0001
Performing Department
(N/A)
Non Technical Summary
This project will significantly expand existing online database resources for tree fruit, berry, nut, and pulse crops by providing access to usable big data aggregated, analyzed, integrated, and visualized, as well as data management and analysis tools. Together with personalized training, this will enable breeders and scientists to optimize the use of cutting-edge big data, tools, and predictive capability to accelerate the pace of research discovery and application in crop improvement. New and improved cultivars and management practices are essential for the specialty crop industry to mitigate a changing environment and provide consumers with access to highly nutritious specialty crop foods. ?
Animal Health Component
70%
Research Effort Categories
Basic
10%
Applied
70%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011119108120%
2010999108120%
2011129108120%
2011212108110%
2011419108110%
2061119104010%
2020999108010%
Knowledge Area
206 - Basic Plant Biology; 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1119 - Deciduous tree fruits, general/other; 1212 - Almond; 1419 - Leguminous vegetables, general/other; 1129 - Berries and cane fruits, general/other; 0999 - Citrus, general/other;

Field Of Science
1040 - Molecular biology; 1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Addressing the economic, environmental, and sustainability challenges facing the U.S. specialty crop industry requires us to accelerate the pace of meaningful discoveries and translate results into efficient and effective crop improvement solutions. Critical to this is turning information into knowledge using insights now afforded by the generation, analysis, and re-use of large and detailed sets of relevant "big data". Scientists in disciplines related to crop improvement in the 25 crops of this project (tree fruit, tree nut, berries, pulses) are now generating these kinds of complex data sets at an exponential rate. We propose expanding the rosaceae, citrus, vaccinium, and pulse crop databases to meet community need for resources with usable big-data aggregated, analyzed, integrated, and visualized as well as data management and analysis tools. Training and outreach in the efficient collection and use of big data, breeding data management systems and databases are integral to these efforts. We will meet these goals through the following objectives:Objective 1: DATA - Collect, curate, and integrate all types of genomics, genetics, and breeding big data in easy-to-use and robust crop-specific databases. (A) Add new content and data types, such as Pan-Genome, Epigenome, and Other Large-Scale Genomic Data; Gene Transcript and Expression Data; Gene/Mutant/Disease Data; GWAS, Trait Locus, and Genetic Map Data; and Large-Scale Phenotypic and Genotypic Data and Germplasm, (B) Analyze big data, including pan-genome, functional annotation of whole genome sequences, biochemical pathways, and synteny among related crops, (C) Improve integration of diverse datasets through curation, analysis, and interface design, and (D) Investigate the potential of AI to improve translation of global predictions for optimizing complex utilization in U.S. breeding programs.?Objective 2: TOOLS - Develop and integrate new or improved tools to promote the collection, integration, and utilization of by scientists and breeders.(A) Expand the Field Book App and BIMS to meet the specific need of specialty crop breeders for improved field data collection, (B) Modify and implement the GOAT community gene curation tool, and (C) Develop a graphical and search viewer for exploring integrated data of genome to phenome across related crops.Objective 3. OUTREACH - Provide scientists and breeders with personalized training in the use of big data, tools, and other resources of the Rosaceae, Citrus, Vaccinium, and Pulse crop databases, and develop and disseminate re-usable, extendable materials for training and broader community outreach.(A) Expert trainers (crop postdocs) deliver on-site and online training on effective and efficient use of the Breeding Information Management System (BIMS), the Field Book App, and the databases, (B) Use communication platforms (social media, newsletters, tutorials, growers meetings, conference presentations, and publications) to disseminate information to all stakeholders, (C) Evaluate the impact of the databases to specialty crop breeding and research outcomes; and (D) Provide support for other specialty crops in using the resource-efficient Tripal database platform
Project Methods
OBJECTIVE 1: DATA - This will involve (1a) Addition of Pan-genome, epigenome, other large-scale genomic data, gene transcript, expression data, gene, mutant, and disease data, GWAS, Trait Locus, and Genetic Map Data, large-scale phenotypic and genotypic data and germplasm data to the databases through collection from NCBI, publications and direct submission from researchers. Various ontologies such as Plant Ontology, Trait Ontology, and Environmental Ontology will be used to annotate plant tissue, traits, and conditions used in the experiments and efficiently integrated with all the other relevant genomic, genetic, and breeding data; (1b) Analysis of big data, including pan-genome, functional annotation of whole genome sequences, biochemical pathways, and synteny among related crops. In addition to hosting pan-genome data generated by researchers, we will perform pan-genome analysis for each species in our database using Pandagma, modified as needed for our analysis/system. We will perform additional analysis of new genome assemblies through computational annotation of the predicted genes with homology to genes of closely related or plant model species and assignment of InterPro protein domains, Gene Ontology terms, and ortholog terms through synteny analysis and KEGG categories. We will align any other genomic features, such as transcripts and genetic markers, to new or updated whole genome sequences when data become available. We will position QTLs from the literature within the current whole genome sequences of each crop. Genomic positions of QTLs will be identified using co-localizing or neighboring markers. We will perform synteny analysis to find conserved syntenic regions among the newest versions of all publicly available high-quality genomes in our databases using MCScanX and the data will be displayed using our Synteny Viewer Whenever a new whole genome data becomes available, we will also construct PlantCyc (metabolic pathway) databases using PathwayTools . The predicted genes from the whole genome sequences will be functionally annotated through a sequence homology search using BLASTX with the UniProtKB/Swiss-Prot and TAIR. BLASTX matches will be parsed, and EC codes transferred to our crop gene models. We will update the Pathway databases as enough new data become available both from the whole genome annotations of our crops and/or the model databases, UniProtKB/Swiss-Prot and TAIR; (1c) Improving the integration of diverse datasets through curation, analysis, and interface design;and (1d) Investigating the potential of AI to improve translation of global predictions for optimizing complex utilization in U.S. breeding programs. Global datasets for almond, blueberry, citrus, and lentil will be accumulated via outreach to U.S. and global communities. Preliminary apple, cherry, peach, and strawberry datasets will be used to develop imputation methods and pipelines, and to identify and resolve issues in global genomic prediction models. This approach will be applied to other project crops as datasets become available. For citrus, we will collaborate with an ongoing U.S. citrus GWAS and genomic selection project to pilot new phenotyping technology, the incorporation of existing data and new data types into the citrus database system, and the use of our technology for genomic prediction of performance for HLB tolerance or resistance, overall plant health, and fruit quality attributes.OBJECTIVE 2: TOOLS - This will involve (2a) Expansion of the Field Book App and BIMS to meet the specific need of specialty crop breeders for improved field data collection - Field Book App will add support for repeated measures/subsampling and create a framework that allows simplified addition of novel trait types such as integrated algorithms, customized crop-specific layouts, and external sensor hardware that are often used as a selection tool in specialty crops (e.g., NIRS, colorimeters). Based on direct feedback, additional apps or features that fill specific breeding informatics gaps will be developed or improved to ensure that breeders can manage their program and data entirely within the BIMS digital breeding ecosystem; (2b) Modifying and implementing the GOAT community gene curation tool - The GOAT software will be modified to make it a Tripal module and to integrate the gene data with other data types and ontologies; and (2c) Developing a graphical and search viewer for exploring integrated data of genome to phenome across related crops by connecting existing tools - Tools to integrate genetic and genomic data will include the extension of the MapViewer tool to display trait-associated markers from GWAS studies on the chromosome next to genetic maps. A GWAS Catalog will be implemented to provide browsing, searching, and graphical display of GWAS data, integrated with marker/gene pages. MapViewer will also be expanded to add an option to display syntenic regions next to the genome viewer, a functionality allowing users to view QTLs and GWAS markers in well-characterized genomes along with the syntenic regions in the crop of interest without the specific QTLs or GWAS markers.OBJECTIVE 3: OUTREACH - This will involve: (3a) Expert trainers (crop postdocs) delivering on-site and online training on effective and efficient use of the Breeding Information Management System (BIMS), the Field Book App, and the databases. This activity will include facilitating the conversion of legacy breeding data into the BIMS; (3b) Use of communication platforms (social media, newsletters, tutorials, growers meetings, conference presentations, and publications) to disseminate information to all stakeholders; (3c) Evaluation of the impact of the databases to specialty crop breeding and research outcomes; (3d) Support for other specialty crops to adopt the resource-efficient Tripal database platform, and; (3e) Implement sustainability plans for the databases (developed through sister project NRSP10).

Progress 09/15/23 to 09/14/24

Outputs
Target Audience:The target audience is predominantly research scientists, breeders, bioinformaticists, database developers, database curators, both national and international, as well as U.S. industry stakeholders from the 25 crops covered in this project. Scientists have been engaged through training workshops, presentations at scientific conferences and meetings, posts to mailing lists, newsletters, webinars, emails about the website, and meetings with advisory groups. Bioinformaticists and database developers have been engaged through participation in monthly meetings on Tripal software, the release of new versions of Tripal and extension modules, the tripal.info website, a two day codefest, monthly Agricultural Biological Database (AgBioData) group meetings, peer-reviewed publications, and presentations at conferences and meetings. Industry stakeholders are being engaged through presentations and interactions at conferences and advisory committee meetings. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training opportunities for researchers (postdocs, early-career scientists), and developers included active participation in workshops, conferences, and meetings, as well as engagement in manuscript writing and various professional development activities, such as short courses and webinars. To foster collaboration and innovation, a BrAPI hackathon and a Tripal codefest were organized, allowing developers to contribute both in person and remotely, working alongside fellow developers from around the world on shared, impactful projects.. How have the results been disseminated to communities of interest?The results of this project have been disseminated through various channels including; 5 Peer-reviewed publications; 32presentations at 7 conferences Plant and Animal Genome Conference National Association of Plant Breeding Annual Meeting Annual Plant Biology Meeting North American Pulse Crop Improvement/Bean Improvement Conference Interational Vaccinium Symposium North American Plant Phenotyping Network Annual Conference ASA, CSSA, SSSATriState Annual Conference Several other smaller meetings including industry 3 database or tools training workshops we organized at major meetings (PAG, NAPB and IVS) 20 newsletters (quarterly for each database) 7 video tutorials Program-specific webinars and in-person training at researchers' locations. What do you plan to do during the next reporting period to accomplish the goals?Here's a plan outlining the next steps for each objective, focusing on actions to be taken during the next reporting period: Objective 1 (DATA): Enhance Data Collection, Curation, and Analysis for Global Performance Prediction Data Expansion: Continue to collect and integrate additional genomic, gentics and breeding data and new data types from peer-reviewed publications, ensuring high-quality data is included for more accurate global performance prediction. Expand the database to include new genetic markers, phenotypic traits, and environmental factors that may impact performance prediction. Genotype and Phenotype Curation: Strengthen data curation efforts, ensuring that the genotype and phenotype data is accurately linked and modeled for performance prediction. Collaborate with researchers to ensure all relevant data sets are properly integrated and curated. Juice Sample Analysis: Conduct further metabolic and phenotypic analysis on juice samples from the University of Florida breeding program, focusing on flavor compounds and their genetic underpinnings. Apply advanced metabolomics and phenotyping techniques to identify key markers associated with flavor traits. Objective 2 (TOOLS): Enhance and Develop Breeding Tools for Better Integration and Prediction FieldBook App and Breeding Information Management Systems (BIMS): Continue improving the user interface and functionality of the FieldBook App to enhance data entry and management for breeders. Further refine and streamline Breeding Information Management Systems (BIMS), ensuring they are more intuitive, faster, and support better data analysis. Enhance the integration with BrAPI resources, ensuring that data can be easily shared and utilized across platforms and organizations. Genome Browser Update: Begin the transition to JBrowse2 for the genome browser, ensuring the new version offers better performance, scalability, and user-friendliness for researchers. GOAT Gene Curation Tool: Begin the process of integrating the GOAT community gene curation tool into the breeding pipeline, allowing for real-time gene annotation and collaborative curation. Performance Prediction Tool: Develop the prototype Genome Prediction Tool, incorporating genomic and phenotypic data to predict breeding outcomes. Conduct initial tests to evaluate the effectiveness and accuracy of predictions made by the tool. Objective 3 (OUTREACH): Continue Dissemination and Training Activities Publications and Presentations: Submit additional peer-reviewed publications that detail new findings, methodology advancements, and the development of tools. Present results at annual conferences and growers' meetings, focusing on the practical applications of the project for the breeding community and growers. Plan for additional presentations at both larger and smaller specialized meetings to reach targeted audiences. Training Workshops and Outreach Activities: Continue organizing and hosting training workshops at major conferences, including PAG, NAPB, and IVS, with a focus on how to use the newly developed tools. Host additional webinars and release new video tutorials to provide remote training to a global audience. Prepare and send out quarterly newsletters for each database, offering updates on new data, features, and tools. Personalized Training: Offer personalized training sessions with breeders, scientists, and other stakeholders, focusing on the practical use of new tools, genomic data, and breeding techniques. Continue engagement with the Database Advisory Board to refine and improve database functionalities based on feedback.

Impacts
What was accomplished under these goals? Objective 1: DATA During the current reporting period, we have made progress on all components (A-D) of Objective 1; Data. 1A and 1C: We have identified, extracted, curated, and integrated a substantial amount of peer-reviewed, publicly available genomic, genetic, and breeding data into our databases for Rosaceae (GDR), Citrus (CGD), Vaccinium (GDV), and Pulse crops (PCD). Unless labeled private, This integrated data is now accessible for browsing, searching, visualization, and downloading through various tools in our databases. Specifically, we have added and integrated: 49 genome sequences; 2,172,087 genes; 2,612,553 mRNAs; 789 germplasm entries; 1,440,890 markers; 34 genetic maps; 7,572 QTLs; 25,716 GWAS results; 6,402,758 genotypic measurements; 13,941 phenotypic measurements; strawberry pangenome; 20 gene expression datasets and 49 BLAST sequence databases. For 1A: Breeding Related Data, the following data was added in either the public BIMS or private BIMS of project breeding programs. Auburn Small Fruit Breeding Program: Established a private Breeding Information Management Systems (BIMS) Program. Collected phenotypic data using the FieldBook App and added blueberry data for 3 trials from 2023 and 2024 and strawberry data from 2024 cultivar evaluation trials. Clemson Peach Breeding Program: Uploaded over 2000 historical tree and fruit photos to Clemson private peach BIMS and collected 3335 field data points via FieldBook app and exported to the BIMS via BrAPI function University of Florida Citrus Breeding Program: Created a private BIMS Program and began populating with data from that program. This included phenotypic data from three breeding trials (1084 citrus accessions, 21 phenotypic traits) and 15 yield and juice related phenotypic traits and 38 drone-phenomics traits measured annually. Newly generated data from this project included genotypic (whole genome sequence) and phenotypic data of 212 diverse citrus accessions under a private-public partnership aimed to discover the nature of genetic resistance/tolerance of citrus to Huanglongbing or citrus greening disease. The DNA samples were sequenced using Illumina 150 bp paired-end reads, with estimated coverage from approximately 15x to 80x. 523,946 SNPs and indels were identified and PCA analysis completed for the population. Phenotypic data is being integrated for GWAS analysis. UF has also assisted the private partner in identifying the significant effects of location, accession and their interactions on major fruit quality traits, including °Brix, limonin content, and juice color. Citrus Community Breeding Data: Established a publicly available Citrus Breeding Program in CGD-BIMS. Added (1) GRIN data program data (959 accessions, 38 traits, 6 trials) and (2) UF-IFAS Citrus Research Rootstock Trials which consolidated historical citrus phenotypic data with a total of 19 traits from a total of 1013 citrus accessions evaluated in several (>10) University of Florida rootstock trials. A total of 360 juice samples from these 212 diverse accessions were received by co-PI Dr. Wang's lab at the end of June 2024, for metabolic and phenotypic analysis of flavor. 1B: Analysis of big-data has included: Biochemical pathways for 15 genomes Gene function annotations for 49 genomes Synteny analysis for 37 genomes Analysis of DNA samples from a private-public partnership (described above) 1C: Global Performance Prediction: The University of Queensland team made progress on Apple Datasets: Ten international datasets for apple were obtained from public data repositories ad (FruitBreedomics, RosBREED), publications (PFR, Liao, Migicovsky) and through collaborations (Howard, QDAFF, Grove, Agroscope, University of Minnesota and Cornell University). Templates called "contribution workbooks" (CWBs) for recording phenotypic, genotypic and meta data for each dataset were created. These CWBs follow a similar format to the existing Breeding Information Management System (BIMS) templates in the Genome Database for Rosaceae (GDR) with some additional information to improve flexibility in capturing and storing data. Harmonization of the heterogeneous datasets was achieved through automatable scripts written in R, ensuring consistency across formats, structures and data types for each CWB. This approach facilitated uniform data aggregation, streamlined edits, and allowed regeneration of CWBs when needed. This allowed efficient management of datasets with traceable, reproducible workflows, and easy and accurate updates to the data while maintaining data integrity. The genotypic information for these datasets were mainly generated from historically commercially available 480K, 50K, 20k and 9K SNP arrays. When collocating the genotypic datasets, using genome location of each marker against the apple reference genome (GDDH13v1.1) in addition to SNP ID, provided robust and uniform genotypic data aggregation across datasets from different platforms. Metadata and genotypic data from the Howard dataset were uploaded into a private program in the GDR BIMS. The Howard dataset will be used as the foundation dataset in this project. A pipeline to curate datasets against the genotypes in the Howard dataset is in progress. Our objective is to obtain at least 20 datasets across the globe for this work and presently, we have obtained 12 datasets from Belgium, Czech Republic, France, Italy, USA, Canada, New Zealand, Australia, and China. We identified additional datasets at JKI (Germany), IRTA (Spain), and CNRS (France). An initial meeting with Andreas Peil and Janne Lempe (JKI, Germany; via Zoom) to obtain the apple data from JKI apple breeding program has been undertaken. We have established a collaborative network with IRTA (Spain) and CNRS (France) to obtain more apple datasets for this project. Established an International consortium to build a Whole genome resequencing (WGR) database and imputation pipeline in apple We obtained a dataset for citrus from Brazil (CCSM), and we are currently collaborating with the University of Florida, USA to obtain citrus datasets. Initial discussions to obtain blueberry data are underway. Objective 2: TOOLS During the reporting period, we made numerous coding improvements to the Field Book App, resulting in 117 issues being closed on GitHub and 130 pull requests being integrated. These updates facilitated the release of v5.6 and features include a completely updated UI to create new traits for data collection, an optimized search feature, development, and improvement of themes to support eInk devices, improvements to the Breeding API integration to facilitate data exchange with compatible databases, and updates to the main collection interface to give more information to breeders as they collect data. We have also made substantial progress toward our v6 release which will improve the analytics available to users as they collect data and is laying the foundation necessary to integrate features specifically for specialty crop breeders who are working across multiple crops. See https://github.com/PhenoApps/Field-Book. A number of improvements were made to the Breeding Information Management System (BIMS, https://www.breedwithbims.org). These included, the ability to load and management image data and repeated measurements (particularly important for speciality crops), addition of new permission levels to facilitate Team Project Management for use in multiple institution projects, compatibility with the Field Book sync function, update of stock types and addition of an administrative function for the BIMS team to notify them when data is added to the BIMS programs, and implementation of a direct link to the BIMS pages.Work on updating BIMS from Drupal 7 to Drupal 10 is now 80% complete and and is on track to be finished by the End of Life of Drupal 7 in January, 2025. Objective 3: Outreach - See Dissemination Section

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2023 Citation: Deng, C. H., Naithani, S., Kumari, S., Cobo-Sim�n, I., Quezada-Rodr�guez, E. H., Skrabisova, M., ... & Jung, S. (2023). Genotype and phenotype data standardization, utilization, and integration in the big data era for agricultural sciences. Database, 2023, baad088.https://doi.org/10.1093/database/baad088
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Clare, S.J., Driskill, M., Millar, T.R., Chagne, D., Montanari, S., Thomson, S., Espley, R.V., Munoz, P., Benevenuto, J., Zhao, D., Sheehan, M., Mengist, M.F., Rowland, L.J., Ashrafi, H., Melmaiee, K., Kulkarni, K.P., Babiker, E.M., Main, D., Olmstead, J.W., Gilbert, J.L., Havlak, P., Hung, H., Kniskern, J., Percival, D., Edger, P., Iorizzo, M., Bassil, N.V. 2024. Development of a targeted genotyping platform for reproducible results within tetraploid and hexaploid blueberry. Frontiers in Horticulture. 2. Article 1339310. https://doi.org/10.3389/fhort.2023.1339310
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Bassil, N.V., King, R., Peterson, M.E., Dossett, M., Hardigan, M.A. 2024. A black raspberry fingerprinting set identifies seedlings in two families. Acta Horticulturae. 1388:115-120. https://doi.org/10.17660/ActaHortic.2024.1388.16
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Hislop, L. M., Luby, C. H., Loarca, J., Humann, J., Hummer, K. E., Bassil, N., ... & Hulse-Kemp, A. M. (2024). A Blueberry (Vaccinium L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research. HortScience, 59(10), 1433-1442. https://doi.org/10.21273/HORTSCI17676-23
  • Type: Theses/Dissertations Status: Published Year Published: 2024 Citation: Edge-Garza, D. (2024) Global genomic prediction in apple PhD thesis. The University of Queensland, Australia.
  • Type: Theses/Dissertations Status: Published Year Published: 2024 Citation: Dajiang Guo (2024) Assessment of genetic diversity and population structure in apple (Malus domestica Borkh.) using SNP markers from 20K SNP chip Masters report. The University of Queensland, Australia.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Rife, TW., C Courtney, B Ellerbrock. (2023 Nov). Field Book: Digital phenotyping for plant breeding. Bean Improvement Cooperative Annual Meeting, November 5-9, Greenville, SC.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: Rife, TW., C Courtney, B Ellerbrock. (2023 Nov). Field Book: Digital phenotyping for plant breeding. Bean Improvement Cooperative Annual Meeting, November 5-9, Greenville, SC.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock. (2024 Jun). PhenoApps for Rice Research Data Collection and Management. International Temperate Rice Conference, June 5-8, New Orleans, LA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jung, S., Lee, T., Gasic, K., & Main, D. (2024). Breeding Information Management System Demonstration. Breeding Tools Workshop part 1. National Association of Plant Breeders Annual Meeting, July 21-25, St. Louis, MO, USA. Oral Presentation
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jung, S., Lee, T., Gasic, K., & Main, D. (2023). Breeding Information Management System Hands-on Training and Discussion. Breeding Tools Workshop part 2. National Association of Plant Breeders Annual Meeting, July 21-25, St. Louis, MO, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock, P Kamath. (2024 Jul). Field Book: Digital phenotyping for plant breeding. National Association of Plant Breeders Annual Meeting, July 21-25, St. Louis, MO. Oral Presentation
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock. (2024 Jan). Field Book: Past, Present, Future.In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Molik, D., Buble, K., Cabugos, L., Campbell, J., Daenzer, J., Raciti, D., Reiser, L., Jung, S., Wright, A., & Yook, K. (2024). FAIR scientific literature is not what you think: How to know where data goes. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jung, S., Lee, T., Cheng, C. H., Humann, J. L., Yu, J., & Gasic, K. (2024). New features of BIMS include interoperability with other resources through BrAPI. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Buble, K., Jung, S., Humann, J. L., Cheng, C. H., Lee, T., Ficklin, S. P., Yu, J., & Main, D. (2024). TripalMap Mapviewer 2.1. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jung, S., & Main, D. (2024, January). Database Resources for Crop Genomics, Genetics and Breeding: NRSP10. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Bushakra, J., Jung, S., Bassil, N., Cheng, C. H., Lee, T., Yu, J., ... & Main, D. (2024, January). Updates on Germplasm and Diversity Data, Crop Ontology Curation, and Search Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Humann, J. L., Jung, S., Lee, T., Cheng, C. H., Zheng, P., Buble, K., ... & Main, D. (2024, January). Updates on Genomic and Transcriptomic Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jung, S., Lee, T., Cheng, C. H., Buble, K., Humann, J. L., Yu, J., ... & Main, D. (2024, January). Updates on Genetics Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Itam, M., Jung, S., Lee, T., Cheng, C. H., Gasic, K., Humann, J. L., ... & Main, D. (2024, January). BreedwithBIMS (Breeding Information Management System) for Crop Breeders. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Manching, H. K., Jung, S., Lee, T., Parsons, T. E., Main, D., Sheehan, M., & Hulse-Kemp, A. M. (2024). Leveraging BrAPI to increase database interoperability - A citrus test case. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Zhang, H., Honaas, L. A., Main, D., & Jung, S. (2024). Building a gene family framework on GDR - Best practice for gene family analysis in non-model plant species. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Main, D., Jung, S., Cheng, C. H., Lee, T., Humann, J. L., Buble, K., Yu, J., Gasic, K., Bassil, N., Ru, S., Peace, C., Coe, M., Ficklin, S. P., & Hardner, C. (2024). Using GDR to enable Rosaceae research - New developments and future directions. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jung, S., Cheng, C. H., Lee, T., Buble, K., Humann, J. L., Zheng, P., Yu, J., Ficklin, S. P., & Main, D. (2024). Building blocks for developing resource-efficient community databases. In Annual Plant Biology Conference, June 21-26, 2024, Honolulu, HI, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Main, D., Jung, S., et al. (2024). Research impact of plant community databases. In Annual Plant Biology Conference, June 21-26, 2024, Honolulu, HI, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Humann, J., Cheng, C.H., Lee, T., Buble, K., Zheng, P., Jung, S., Yu, J., Gasic, K., Ru, S., Bassil, N., Iorizzo, M. & Main, D. (2024, August). Genome Database for Vaccinium: A community resource for genetics, genomics, and breeding research. In 13th International Vaccinium Symposium. Halifax, Nova Scotia, Canada. Oral Presentation.
  • Type: Other Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock, P Kamath. (2024 Aug). Field Book: Overview and Features. Plant Germplasm Operations Committee. Davis, CA.
  • Type: Other Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock, P Kamath. (2024 Aug). Digitizing Plant Breeding and Genetics Data Collection. Justus Liebig University Giessen. Giessen, Germany.
  • Type: Other Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock. (2024 Apr). Development of robust imaging platforms for routine phenotyping in Field Book. Agricultural Genome to Phenome Initiative Field Day. Virtual.
  • Type: Other Status: Published Year Published: 2024 Citation: Rife, TW., C Courtney, B Ellerbrock, P Kamath. (2023 Nov). Cultivating digital data collection tools that promote the growth of modern breeding programs. North Carolina State University.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Tello-Ruiz, M. K., Ali, K., Ali G. S., Bassil, N. V., Beier, S., Bushakra, J., Cobo-Simon, I., Ware, D., Wei, S., Cezard, T., Dyer, S., Gutierrez, O. A., Harrison, M. L., Humann, J., Kumar, V., Nelson, R., Salavati, M., & Sheehan, M. (2024). Standardizing biocuration of genetic variation data to promote FAIRification. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Bassil, N., Hislop, L., Hulse-Kemp, A., Zhang, D., Sheehan, M., Human, J., Main, D., et al. (2024, January). Developing a new crop ontology for blueberry. In Plant and Animal Genome Conference/PAG 31 (January 12-17, 2024), San Diego, USA. Oral Presentation.
  • Type: Other Status: Published Year Published: 2023 Citation: Tapia, R. (2023) Genomics-able tools and its application in citrus breeding. UF/IFAS Citrus Research and Education Center Fall Seminar Series., October 13, 2023. Lake Alfred, Florida, USA.
  • Type: Websites Status: Published Year Published: 2024 Citation: https://fruitandnutlist.org
  • Type: Websites Status: Published Year Published: 2024 Citation: htps://www.agbiodata.org


Progress 09/15/22 to 09/14/23

Outputs
Target Audience:The target audience is predominantly rseearch scientists, breeders, bioinformaticists, database developers, database curators, both national and international, as well as, U.S. industry stakeholders from the 25 crops covered in this project. Scientists have been engaged through training workshops, presentations at scientific conferences and meetings, monthly mailing list posts, quarterly newesletters, webinars, emails about the website, and meetings with advisory groups. Bioinformaticists and database developers have been engaged through participation in monthly meetings on Tripal software, the release of new versions of Tripal and extension modules, the tripal.info website, a two day Tripal codefest, a two day BrAPIhackathon, monthly Agricultural Biological Database (AgBioData) group meetings, peer-reviewed publications, and presentations at conferences and meetings. Industry stakeholders are being engaged through presentations and interactions at coferencesand advisory committee meetings. Changes/Problems:Due to delays in getting funding to sub contract instituitions we were not able to hire the crop postdocs until later in year 1 and are still trying to recruit one for a joint pulse/citrus curation position at WSU. Hurricanes severly impacted the population of citrus being used for GWAS studies and we are discussing alternative populations as a substitute. What opportunities for training and professional development has the project provided?Training opportunities for researchers (postdocs, early career scientists)anddevelopersincluded participation and presentation at workshops, conferences and meetings, as well as manuscript writing and participation in short courses. A BraPI hackathon and Tripal codefest enabled developers to contribute in person or remotely to work with other developers from across the world on shared projects. How have the results been disseminated to communities of interest?Through 4 training workshops at the major conferences for the community (PAG, ASHS, NAPB, Rosaceae biennial International Conference), 11 oral and 9 poster presentations at conferences,monthly community emails for each database (quarterly newsletters for each database, 7 "how to" videos, and a "year in review"), database and BIMS brochures at every conference or meeting, training webinars, 4 advisoryboard meetings, and twitter. What do you plan to do during the next reporting period to accomplish the goals? DATA: We will ramp up data curation and ingest of genomics, genetics, and breeding data to the databases now that we have most of the crop postdocs hired and trained. We will also collect and curate data for performance prediction modeling efforts and decide on a final plan to deal with issues of data collection for citrus phenotyping which was impacted by hurricanes in the research trial populations in Florida. TOOLS: We will start work on modifying and implementing the GOAT community gene curation tool, add repeated measures functionality to BIMS, add geo-navigation plot/tree identification to Field Book, and work on global performance prediction modeling. OUTREACH: We will conduct in-person program outreach training on using BIMS, FieldBook and the databases (made possible now that we have most of the crop postdocs hired and trained) as well as hold training workshops at conferences, presentations and posters at conferences and meetings, do "How to" videos, newsletter, meet with the project advisory committee, as well as database advisory committees, and submit manuscripts for CGD, GDV, PCD to peer-reviewed journals.

Impacts
What was accomplished under these goals? Objective 1:DATA -Collect, curate, and integrate all types of genomics, genetics, and breeding big data in easy-to-use and robust crop-specific databases. In year 1 of this award we added genomic, genetic and breeding data to our rosaceae (GDR), citrus (CGD), vaccinium (GDV) and pulse crop (PCD) databases. In total we have added 54 genome sequences, 3,773,154 genes, 4,090,430 mRNAs, 52,971 germplasm, 6,194 genotypes, 256,193 markers, 23 genetic maps, 1028 QTL/MTL, and 158 species. As per our stated objective 1A, we also added new data types for many of our databases. These included GWAS, methylation, expression, haplotype, and pan genome data. As part of objective 1B, we performed computational analysis on genes and synteny analysis for all new genomes which are then made searchable via our updated MegaSearch tool and synteny/genome viewers. Breeders using our Breeding Information Management System (BIMS) continued to add phenotypic data to their private breeding programs, with most using the Field Book App to collect and transfer these data to their BIMS accounts. Co-PI's Gmitter (Florida) and Ru (Auburn) started using the BIMS for their program with data upload and assessment ongoing, while Co-PI Gasic (Clemson), a long-term user of BIMS, continued to upload phenotypic and genotypic data to her program. High-throughput phenotyping for the citrus GWAS project was started with data collected by drone for canopy width and NDVI. For Objective 1D, work was started by Co-PI Hardner (Queensland) on working with collaborators to obtain phenotype and genotype datasets to assess inclusion in global performance prediction for various fruit crops. Work on crop ontology development for strawberry was initiated by Co-PI's Bassil and Ru (Auburn). Objective 2: TOOLS -Develop and integrate new or improved tools to promote the collection,integration, and utilization of by scientists and breeders. In year 1 of this award, Co-PI Rife was able to recruit a developer to start working on improvements to the Field Book App for specialty crop breeders. Field Book has been further developed with new features. Repeated measures have been added which allows plant breeders to easily collect multiple phenotypes per trait-entry. Themes have been added to adjust the size of fonts and modify the app color scheme which will allow better support on eInk devices that have better outdoor visibility and increased battery life. The delivery of new versions of Field Book have been automated using GitHub actions allowing faster turnaround to fix issues and integrate new features. A number of improvements were made for the Breeding Information Manage System (BIMS). These included, enabling Trait descriptor export (BIMS-Field Book) through BrAPI, implicit grant authorization added from BIMS to FieldBook, BIMS/MCL made compatible with PHP8, and a standalone BreedwithBIMS program (www.breedwithbims.org) was created to allow any plant breeder to use BIMS (so independent of our integrated database BIMS). Work was started to enable image upload in BIMS. In other work, the gene expression module was modified for biomaterial page inclusion, New data templates were created for GWAS data submission and GWAS data search was added to MegaSearch and GWAS viewing functionality in MapViewer. Objective 3. OUTREACH -Provide scientists and breeders with personalized training in the use of big data, tools, and other resources of the Rosaceae, Citrus, Vaccinium, and Pulse crop databases, and develop and disseminate re-usable, extendable materials for training and broader community outreach. Despite delays in hiring crop postdocs for data curation and outreach In year 1 of this award, considerable effort was made by the project team on outreach and training to showcase the databases and tools of this project. This included workshops at four conferences:" Database Resources for Crop Genomics, Genetics and Breeding Workshop": at the 2023 International Plant and Animal Genome Conference (January, 2023); "GDR Training Workshop" at the International Rosaceae Genomics Conference (March, 2023); "Breeding Tools Workshop" at the National Association of Plant Breeding Annual Meeting (July, 2023); and "Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Databases Workshop" at the American Society for Horticultural Science Annual Conference (August, 2023). These events were well attended, with excellent feedback provided by participants. To increase the connectivity between Field Book and external database systems like BIMS, Clemson hosted the Breeding API hackathon in March 2023. Field Book developers worked with WSU to ensure BrAPI compatibility and connectivity would remain robust after recent version updates. In addition to our training workshops, we also gave a total of 11 oral and 9 poster presentations at three of these conferences in relevant sessions. For all these conferences we brought and disseminated brochures for the databases. We have monthly emails to each of our database communities. These included 7 short "How to" videos regarding using the resources in the databases, 4 quarterly newsletters for each database highlighting new data, features, and community news, etc, and a happy holidays, end of calendar year flyer summarizing the year in review for each database. We also held online training for several groups who wanted dedicated training. Training materials were updated for all our databases, BIMS and FieldBook. The PhenoApps project website (phenoapps.org) was updated with hardware suggestions and a contact form to enable requests for new/improved features and get technical help. Field Book v5.4 documentation was moved online to https://docs.fieldbook.phenoapps.org. The manual for BIMS was updated and made available on the homepage of www.breedwithbims.org. We were happy to have 2 groups successfully create BIMS programs just by using the manual. BIMS is to our knowledge the only free, online breeding data management program that enables breeders to fully manage their own breeding programs, including all data upload.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, Jung S, Cheng CH, Lee T, Buble K, Gasic K,. & and Zheng P. 2023. Twenty Years of GDR. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, and Jung S. 2023. Sustainability Efforts of NRSP-10. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Humann J, Cheng CH, Crabb J, Jung S, and Main D. 2023. Managing Data Curation from Publications with the Tripal Pub Curator Module. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Humann J, Jung S, Lee T, Cheng CH, Zheng P, Buble K,. & Main D. 2023. Updates on Genomic Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Bassil N, Jung S, Cheng CH, Lee T, Yu J, Humann J,. & Main D. 2023. Updates on Germplasm and Diversity Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gasic K, Campbell T, Lee T, McGee RJ, Jung S, Humann J,. & Main D. 2023. A Peach Breeders Perspective on Using the Breeding Information Management System for Crop Breeding. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Buble K, Cheng CH, Lee T, Yu J, Humann J,. & Main D. 2023. Updates on Genetics Data and Tools in Rosaceae, Cotton, Citrus, Vaccinium and Pulse Crop Databases. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Humann J, Cheng CH, Lee T, Bubble K, Jung S, Iorizzo M,. .. Main D. 2023. The Genome Database for Vaccinium: Data and Tools for Genetics, Genomics, and Breeding Research. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Ma Y, Main D, Burrows M, Heineck G, Porter L, Coyne C, and McGee RJ. 2023. Resequencing of 238 Lentil Accessions Provides Insights Into Diversity, Domestication, and Genetic Basis of Important Traits. Plant and Animal Genome Conference, January 13-18, 2023, San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, Jung S, Cheng CH, Lee T, Buble K, Gasic, K & and Zheng P. 2023. Twenty Years of GDR. International Rosaceae Genomics Conference, March 13-16, 2023, Nelson, NZ.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Cheng CH, Lee T, Buble K, Zheng P, Gasic, K & and Main D. 2023. Updates on the Breeding Information Management System (BIMS) in GDR. International Rosaceae Genomics Conference, March 13-16, 2023, Nelson, NZ.
  • Type: Other Status: Published Year Published: 2023 Citation: Jung S, Cheng CH, Lee T, Buble K, Zheng P, Gasic K,. & and Main D. 2023. GDR Training Workshop. International Rosaceae Genomics Conference, March 13-16, 2023, Nelson, NZ.
  • Type: Other Status: Published Year Published: 2023 Citation: Genome Database for Rosaceae Brochure. 2023. International Rosaceae Genomics Conference, March 13-16, 2023, Nelson, NZ.
  • Type: Other Status: Published Year Published: 2023 Citation: Breeding Information Management Brochure. 2023. International Rosaceae Genomics Conference, March 13-16, 2023, Nelson, NZ.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Lee T, Gasic K, and Main D. 2023. Breeding Information Management System Demonstration. Breeding Tools Workshop part 1. NAPB 2023 Annual Meeting, July 16-August 20, 2023, Greenville, SC, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Lee T, Gasic K, and Main D. 2023. Breeding Information Management System Hands on Training and Discussion. Breeding Tools Workshop part 2. NAPB 2023 Annual Meeting, July 16-August 20, 2023, Greenville, SC, USA.
  • Type: Other Status: Published Year Published: 2023 Citation: Breeding Information Management Brochure. 2023. NAPB 2023 Annual Meeting, July 16-August 20, 2023, Greenville, SC, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, Jung S, Cheng CH, Lee T, Buble K, Humann J., & and Zheng P. 2023. Data and Tools in Specialty Crop Databases: Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Database Workshop. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, Jung S, Cheng CH, Lee T, Buble K, Humann J., & and Zheng P. 2023. Introduction to Specialty Crop Databases: Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Database Workshop. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Cheng CH, Lee T, Buble K, Humann J, Zheng P., & and Main D. 2023. Use case Demonstration - Specialty Crop databases: Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Database Workshop. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Cheng CH, Lee T, Buble K, Humann J, Zheng P., & and Main D. 2023. How to Submit Research Data: Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Database Workshop. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, Jung S, Cheng CH, Lee T, Buble K, Humann J., & and Zheng P. 2023. Discussion on how to improve specialty crop databases: Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Database Workshop. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jung S, Lee T, Gasic K, Humann J, Yu J, Main D. Breeding Information Management System (BIMS) for Crop Breeders. Vegetable Breeding 1 - Oral Session. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Main D, Jung S, Cheng CH, Lee T, Buble K, Humann J., & and Gasic K. 2023. Advancing Fruit Breeding Research through GDR: An Integrated Database Resource for Rosaceae Genomics, Genetics, and Breeding. Fruit Breeding 1 - Oral Session. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Bassil N, Driskill M, Clare S, Zheng P, Chagne D, Montanari S., & and Patrick Edger. 2023. VacCAP Develops High Throughput Genotyping Platforms for Blueberry and Cranberry. Fruit Breeding- Oral Session 2. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Cheng CH, Jung S, Lee T, Buble K, Humann J, Zheng P., ... and Main D. 2023. Open-Source Solutions for Efficiently Building Community Databases for Crop Genomics, Genetics, and Breeding Research. Poster Presentation. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Gasic K, Jung S, Cheng CH, Lee T, Buble K, Humann J., & and Main D. 2023. Use case Demonstration - Breeding Information Management System (BIMS): Hands-on Training for Effective Use, Data Contribution, and Options for Long Term Sustainability of Specialty Crop Community Database Workshop. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Buble K, Gasic K, Karp D, Stover-Blackburn J, and Main D. 2023. Advancing Fruit Breeding Research through GDR: An Integrated Database Resource for Rosaceae Genomics, Genetics, and Breeding. Poster. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Other Status: Published Year Published: 2023 Citation: Genome Database for Vaccinium Brochure. 2023. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA.
  • Type: Other Status: Published Year Published: 2023 Citation: Genome Database for Rosaceae Brochure. 2023. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA
  • Type: Other Status: Published Year Published: 2023 Citation: Citrus Genome Database Brochure. 2023. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA
  • Type: Other Status: Published Year Published: 2023 Citation: Breeding Information Management Brochure. 2023. ASHS 2023 Annual Conference, July 31-August 4, 2023, Orlando, FL, USA
  • Type: Websites Status: Published Year Published: 2023 Citation: PhenoApps website (phenoapps.org).