• Maize Phenotypic Datasets


    The Seeds of Discovery project has generated a number of phenotypic datasets for maize germplasm including accessions in CIMMYT’s germplasm bank (CGB), test crosses and pre-breeding materials generated using materials from the CGB. Trials have been grown under optimal conditions as well as under abiotic stress conditions including drought and heat, and under biotic stress conditions including Tar Spot and Turcicum disease pressure.

    Product details and features

    In field trials, standard traits such as yield, flowering time, lodging, and plant and ear height have been routinely captured. Additional traits, such as disease resistance scores, have been recorded in specialized trials. Maize quality traits, such as grain protein and oil content, have also been measured for selected germplasm.

    Phenotypic data are released in the Dataverse repository that stores flat files and/or the Germinate data warehouse that stores the phenotypic results in a queryable and subsettable format that can link these data to additional genotypic data and germplasm information. In general, analyzed results for each location for each experiment are released as individual datasets within Germinate. Phenotypic data are primarily released in Dataverse when additional supporting files or explanations of experimental conditions are required.


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  • Germinate Phenotypic Datasets:

    1. A list of more than 30 phenotypic datasets available in the Germinate data warehouse provides links to individual datasets.Link
    2. Each dataset is available for direct download in a simple text format that includes germplasm identifiers, trait names and units, and phenotypic values.
    3. Phenotypic datasets may also be generated dynamically in a number of ways such as:
      • Users can search across all phenotypic data and filter to selected data points based on several criteria including germplasm ID, trait name, trait values, and dataset descriptions
      • Users can generate “Groups” of germplasm using one or more search or filtering tools and use them to retrieve phenotypic data from one or more trials
      • Users can download selected traits from any trial or set of trials
    4. Phenotypic data from one or more trials can also be visualized on graphs that allow users to select subsets of germplasm based on their phenotypic values.
    5. Phenotypic data files are exported in a format that make them ready for upload in the Flapjack software where they can be combined with genotypic data.


    Dataverse Phenotypic Datasets:

    1. A list of phenotypic datasets available for download in the Dataverse repository provides links to individual studies.Link
    2. Studies contain fixed data files including the phenotypic results file(s), and supporting files such as field maps, management sheets, weather data, phenotyping protocols, or other relevant documents.
    3. Each study is annotated with standard study-level metadata including: study title, description, authors, data generators, date of generation, keywords, crop ontology terms for traits, links to related studies, links to relevant journal articles

    Comments

    The phenotypic datasets in Germinate primarily contain analyzed BLUPs but it is important to use the dataset description to determine the type of data (raw or analyzed) and treatment conditions applied in the trial. Please contact Cimmyt-mab-seed@cgiar.org for additional help with accessing or working with any of these phenotypic data files.


     


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  • Primary Users

    Maize pre-breeders, researchers, and students working in relevant fields such as biology, breeding, and bioinformatics, as well as germplasm bank curators and users of CIMMYT’s germplasm bank materials.

     

    Availability

    Phenotypic Datasets in Germinate: http://germinate.seedsofdiscovery.org/maize/#categorical-datasets

    Phenotypic Datasets in Dataverse: http://data.cimmyt.org/dvn/dv/seedsofdiscoverydvn/faces/StudyListingPage.xhtml?mode=1&collectionId=14

     

    For more information

     


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