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Breedbase

dataset
posted on 2023-12-18, 18:18 authored by Lukas A. Mueller, Naama Menda, Susan R. Strickler, Surya Saha, Nicolas Morales, Mirella Flores, Isaak Y. Tecle, Noe Fernandez-Pozo, Guillaume Bauchet, Alex Ogbonna, Tom York, Hartmut Foerster, Bryan Ellerbrock, Prashant Hosmani

Breedbase is a web-based, comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high density genotypic information, and provide Genomic Selection related analyses and predictions. Breedbase supports the Breeding Application Programming Interface (BrAPI) standard which defines data objects and methods for exchanging breeding data. The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see RTBbase.org). There are a number of instances running for diverse crops, including Cassava (https://cassavabase.org, sweet potato (https://sweetpotatobase.org), banana (https://musabase.org), rice (https://ricebase.org), tomato and other Solanaceae (https://solgenomics.net/) and many others. The Breedbase manual provides detailed information about available features.


Resources in this dataset:

  • Resource Title: Website Pointer for Breedbase.

    File Name: Web Page, url: https://breedbase.org/

    Search utilities: Wizard; Accessions and Plots; Organisms; Progenies and Crosses; Field Trials; Genotyping Plates; Genotyping Data Projects; Genotyping Protocols; Traits; Images; People; FAQ.

    Manage utilities: User Roles; Breeding Programs; Locations; Accessions; Seed Lots; Crosses; Field Trials; Genotyping Trials; Field Book App; Phenotyping; Barcodes; Label Designer; Download; Upload; ODK Data Collection.

    Analyze utilities: Breeder Tools -- Selection Index; Genomic Selection; Population Structure; Accession Usage; Compare Trials; Graphical Filtering Sequence Analysis -- BLAST; VIGS Tool; HapMap Jbrowse Other -- Ontology Browser; Compose a New Trait.

Funding

USDA-NIFA: USDA CSREES 2007-02777; SolCAP - Solanaceae Coordinated Agricultural Project

Cornell University

United States - Israel Binational Agricultural Research and Development Fund: FI-370-2005

National Science Foundation: 0606595

National Science Foundation: 0820612

National Science Foundation: 0421634

National Science Foundation: 0116076

National Science Foundation: 9975866

National Science Foundation: 9872617

History

Data contact name

Sol Genomics Network

Data contact email

sgn-feedback@sgn.cornell.edu

Publisher

Boyce Thompson Institute for Plant Research, Cornell University

Temporal Extent Start Date

2005-01-01

Theme

  • Not specified

Geographic Coverage

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ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

genomics; databases; tomatoes; potatoes; tobacco; eggplants; Coffea; expressed sequence tags; unigenes; complementary DNA; sequence homology; microarray technology; bioinformatics; biochemical pathways; phylogeny; gene silencing; phenotype; loci; Solanaceae; Petunia hybrida; Rubiaceae; peppers; breeding; computer software; genotyping; marker-assisted selection; prediction; crops; cassava; sweet potatoes; bananas; rice; selection methods; field crops; crop management; data collection; application programming interface; crossing; field experimentation; people; breeding programs; barcoding; selection index; population structure; sequence analysis

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Mueller, Lukas A.; Menda, Naama; Strickler, Susan R.; Saha, Surya; Morales, Nicolas; Flores, Mirella; Tecle, Isaak Y.; Fernandez-Pozo, Noe; Bauchet, Guillaume; Ogbonna, Alex; York, Tom; Foerster, Hartmut; Ellerbrock, Bryan; Hosmani, Prashant (2019). Breedbase. Boyce Thompson Institute for Plant Research, Cornell University.

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    Categories

    Keywords

    NP301BreedbaseOnline databasedata.govARS

    Licence

    CC BY 4.0

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