AGILE Activity 5: Breeders' Toolbox

AGILE Activity 5: Breeders' Toolbox


Throughout the AGILE project, KnowPulse has acted as the official data warehouse for the wealth of data generated. These data can be accessed through the specific research projects linked to on the main AGILE page, as well as, within tools and searches accessible from the frontpage. As data are published, it will become accessible to the public for analysis and exploration through KnowPulse.


  • The cultivated lentil Genome Browser (JBrowse) was developed under AGILE and includes RNA-seq-derived gene models, as well as markers developed through AGILE activities. Furthermore, regions of variability amongst wild lentil species , and regions of inferred homology to other legumes (such as Medicago and soybean) will be highlighted, providing breeders with context to evaluate marker usability for their germplasm of interest.
  • The BLAST service available through KnowPulse has been extended to include the Lcu genome assembly and the wild lentil de novo assemblies generated through AGILE. This provides the legume community with a means of finding regions in lentil homologous to specific genes of interest and results are linked to the genome browser to provide context and a pool of possible markers for testing by researchers.
  • The genotype matrix tool has been populated with the Lentil Diversity Panel exome capture dataset developed through AGILE, which provides direct access to genotypic data for specific lines and/or markers of interest. Additionally, all genotypic datasets generated through AGILE have been made available to collaborators through the VCF Bulk export tool which facilitates analysis by researchers by providing filter functionality with results available in a variety of formats.
  • Support for phenotypic data for all crops within KnowPulse has been developed through AGILE and includes trait pages, as well as a trait distribution tool for visualizing available data. Phenotypic data is also available on germplasm pages providing important information to breeders to inform crossing decisions.
  • Genetic map and quantitative trait loci (QTL) storage and visualization have been added to KnowPulse under AGILE to complete the genotype to phenotype link. These resources being made available in the same resource ensures that researchers can confirm both genotypic and phenotypic data used to determine QTL came from the same germplasm collection and greatly facilitate marker identification for use in breeding programs.
  • Semantic web-ready Tripal Content web services ensure the same data available to researchers through content pages are also available for programmatic exploration and tool integration. This extends the availability of AGILE datasets beyond KnowPulse to the greater legume community.

Additional information including screenshots is available through the linked publications. All tools developed under AGILE are open-source and freely available through github.

Published Materials
  1. Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP. Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Database. July 2019, 2019: baz077
  2. Sanderson L-A, Caron CT, Tan R, Shen Y, Liu R and Bett KE (2019) KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement. Front. Plant Sci. 10:965. doi: 10.3389/fpls.2019.00965